Genome Sequence Paper Title Generator

So, you and several dozen totally essential collaborators have been hard at work sequencing the genome of a super important species, and you’re ready to write up your results. Between doing the same analyses as every other genome sequencing study and overselling the novelty and significance of your results, you probably don’t have time to waste on something as trivial as the title of your paper.  Not having any particular hypothesis or well-reasoned research question in mind can also make it difficult to know how to package your paper for publication.

Luckily, the new “Genome Sequence Paper Title Generator” is here to help!  Simply fill in the details below, and you’re good to go!

Genome Sequence Paper Title Generator v.1.0

1) Type of genome sequence (optional): i) Draft, ii) Whole, iii) Comparative, iv) Do not specify

2) Species name: ____________________

3) Major contribution: i) Reveals, ii) Provides insights into

4) Novelty modifier (optional): i) Novel, ii) New, iii) Unique, iv) None

5) Ad-hoc focus of research: i) Notable physical, physiological, or behavioural trait of species, ii) Adaptation to environment of species, iii) Medical or industrial significance of species, iv) Features of genome of species

 


Revealing stuff through genome sequencing.

Maybe you thought a lot of genome papers provide “insights” — and you’d be right. But did you know that even more genome papers “reveal” stuff? It’s true! Here’s a list of nearly 500 examples.

Abe, A., et al. (2012). “Genome sequencing reveals agronomically important loci in rice using MutMap.” Nature Biotechnology 30(2): 174-178.

Acarkan, A., et al. (2000). “Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella.” Plant Journal 23(1): 55-62.

Ahola, V., et al. (2014). “The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.” Nature Communications 5.

Aklujkar, M., et al. (2012). “The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.” Bmc Genomics 13.

Alcaraz, L. D., et al. (2008). “The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.” Proceedings of the National Academy of Sciences of the United States of America 105(15): 5803-5808.

Alexander, L. W. and K. E. Woeste (2014). “Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management.” Tree Genetics & Genomes 10(4): 803-812.

Almeida, N. F., et al. (2009). “A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000.” Molecular Plant-Microbe Interactions 22(1): 52-62.

Ammayappan, A. and V. N. Vakharia (2009). “Complete Nucleotide Analysis of the Structural Genome of the Infectious Bronchitis Virus Strain Md27 Reveals its Mosaic Nature.” Viruses-Basel 1(3): 1166-1177.

Andersen, M. T., et al. (2013). “Comparison of the complete genome sequence of two closely related isolates of ‘Candidatus Phytoplasma australiense’ reveals genome plasticity.” Bmc Genomics 14.

Anderson, I., et al. (2008). “Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.” Journal of Bacteriology 190(8): 2957-2965.

Anderson, I. J., et al. (2009). “The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.” Bmc Genomics 10.

Andrade, B. G. N., et al. (2014). “The genome of a clinical Klebsiella variicola strain reveals virulence-associated traits and a pl9-like plasmid.” Fems Microbiology Letters 360(1): 13-16.

Arraes, F. B. M., et al. (2007). “Differential metabolism of Mycoplasma species as revealed by their genomes.” Genetics and Molecular Biology 30(1): 182-189.

Ash, K., et al. (2014). “A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential.” Open biology 4(10).

Ashelford, K., et al. (2011). “Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis.” Genome Biology 12(3).

Atanur, S. S., et al. (2013). “Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat.” Cell 154(3): 691-703.

Axelsson, E., et al. (2005). “Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.” Genome Research 15(1): 120-125.

Ayala-del-Rio, H. L., et al. (2010). “The Genome Sequence of Psychrobacter arcticus 273-4, a Psychroactive Siberian Permafrost Bacterium, Reveals Mechanisms for Adaptation to Low-Temperature Growth.” Applied and Environmental Microbiology 76(7): 2304-2312.

Aylward, F. O., et al. (2013). “Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities.” Applied and Environmental Microbiology 79(12): 3724-3733.

Azcarate-Peril, M. A., et al. (2008). “Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism.” Applied and Environmental Microbiology 74(15): 4610-4625.

Azuma, Y., et al. (2009). “Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus.” Nucleic Acids Research 37(17): 5768-5783.

Baek, K. T., et al. (2013). “Genetic Variation in the Staphylococcus aureus 8325 Strain Lineage Revealed by Whole-Genome Sequencing.” PLoS ONE 8(9).

Ballvora, A., et al. (2007). “Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments.” Bmc Genomics 8.

Banyai, K., et al. (2014). “Whole-genome sequencing of a green bush viper reovirus reveals a shared evolutionary history between reptilian and unusual mammalian orthoreoviruses.” Archives of Virology 159(1): 153-158.

Barry, J. D., et al. (2005). “What the genome sequence is revealing about trypanosome antigenic variation.” Biochemical Society Transactions 33: 986-989.

Barth, D. and T. U. Berendonk (2011). “The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium.” Bmc Genomics 12.

Bellgard, M. I., et al. (2009). “Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira hyodysenteriae Reveals Adaptations to Its Lifestyle in the Porcine Large Intestine.” PLoS ONE 4(3).

Bentley, S. D., et al. (2012). “The Genome of Mycobacterium Africanum West African 2 Reveals a Lineage-Specific Locus and Genome Erosion Common to the M. tuberculosis Complex.” Plos Neglected Tropical Diseases 6(2).

Berg Miller, M. E., et al. (2009). “Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.” PLoS ONE 4(8): e6650-e6650.

Biggs, P. J., et al. (2011). “Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage.” PLoS ONE 6(11): e27121 [27114pp.]-e27121 [27114pp.].

Bishop-Lilly, K. A., et al. (2012). “Whole genome sequencing of phage resistant Bacillus anthracis mutants reveals an essential role for cell surface anchoring protein CsaB in phage AP50c adsorption.” Virology Journal 9.

Bitton, D. A., et al. (2011). “Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability.” Genetics 187(4): 1207-U1369.

Blanc, G., et al. (2012). “The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.” Genome Biology 13(5).

Blanc, G., et al. (2010). “The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex.” Plant Cell 22(9): 2943-2955.

Boekhorst, J., et al. (2004). “The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content.” Microbiology-Sgm 150: 3601-3611.

Bogen, C., et al. (2013). “Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production.” Bmc Genomics 14.

Bontell, I. L., et al. (2009). “Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants.” Genome Biology 10(5).

Borneman, A. R., et al. (2011). “Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae.” PLoS genetics 7(2).

Borneman, A. R., et al. (2012). “The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins.” FEMS Yeast Research 12(1): 88-96.

Borneman, A. R., et al. (2012). “Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.” Bmc Genomics 13.

Bos, K. I., et al. (2014). “Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.” Nature 514(7523): 494-+.

Bottacini, F., et al. (2012). “Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut.” PLoS ONE 7(9).

Bowler, C., et al. (2008). “The Phaeodactylum genome reveals the evolutionary history of diatom genomes.” Nature 456(7219): 239-244.

Bradbury, J. (1997). “Helicobacter pylori genome sequence reveals potential new drug targets.” Lancet 350(9075): 415-415.

Bradel, B. G., et al. (2000). “Sequence analysis and genome organisation of poinsettia mosaic virus (PnMV) reveal closer relationship to marafiviruses than to tymoviruses.” Virology 271(2): 289-297.

Brayton, K. A., et al. (2005). “Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins.” Proceedings of the National Academy of Sciences of the United States of America 102(3): 844-849.

Brazilian National Genome Project, C. (2003). “The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability.” Proceedings of the National Academy of Sciences of the United States of America 100(20): 11660-11665.

Bridger, S. L., et al. (2012). “Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.” Journal of Bacteriology 194(15): 4097-4106.

Brzuszkiewicz, E., et al. (2013). “Legionella oakridgensis ATCC 33761 genome sequence and phenotypic characterization reveals its replication capacity in amoebae.” International Journal of Medical Microbiology 303(8): 514-528.

Brzuszkiewicz, E., et al. (2011). “Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC).” Archives of Microbiology 193(12): 883-891.

Burkhart, C. N. and C. G. Burkhart (2006). “Genome sequence of Propionibacterium acnes reveals immunogenic and surface-associated genes confirming existence of the acne biofilm.” International Journal of Dermatology 45(7): 872-872.

Campo, D., et al. (2013). “Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection.” Molecular Ecology 22(20): 5084-5097.

Canovas, D., et al. (2003). “Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis.” Environmental Microbiology 5(12): 1242-1256.

Cantu, D., et al. (2013). “Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors.” Bmc Genomics 14.

Cao, Z., et al. (2013). “The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods.” Nature Communications 4.

Carneiro, M., et al. (2014). “Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.” Science 345(6200): 1074-1079.

Carvalho, C. M., et al. (2012). “The genome and proteome of a Campylobacter coli bacteriophage vB_CcoM-IBB_35 reveal unusual features.” Virology Journal 9.

Caspermeyer, J. (2014). “New Analysis of Seven Ant Genomes Reveals Clues to Longer Life Spans Associated with Sociality.” Molecular Biology and Evolution 31(7): 1937-1937.

Castoe, T. A., et al. (2014). “The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (vol 110, pg 20645, 2013).” Proceedings of the National Academy of Sciences of the United States of America 111(8): 3194-3194.

Causse, M., et al. (2013). “Whole genome resequencing in tomato reveals variation associated with introgression and breeding events.” Bmc Genomics 14.

Chao, D.-Y., et al. (2005). “Strategically examining the full-genome of dengue virus type 3 in clinical isolates reveals its mutation spectra.” Virology Journal 2.

Charkowski, A. O. (2007). Potential Disease Control Strategies Revealed by Genome Sequencing and Functional Genetics of Plant Pathogenic Bacteria.

Chau, R., et al. (2012). “Genome of an octopus-derived Pseudoalteromonas reveals unprecedented natural product biosynthesis gene clusters.” Planta Medica 78(11): 1057-1057.

Chavez-Galarza, J., et al. (2013). “Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms.” Molecular Ecology 22(23): 5890-5907.

Chen, C., et al. (2013). “Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors.” Bmc Genomics 14.

Chen, J., et al. (2013). “Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.” Nature Communications 4.

Chen, X. H., et al. (2009). “Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens.” Journal of Biotechnology 140(1-2): 27-37.

Chen, Y., et al. (2013). “Whole-Genome Sequencing of Gentamicin-Resistant Campylobacter coli Isolated from US Retail Meats Reveals Novel Plasmid-Mediated Aminoglycoside Resistance Genes.” Antimicrobial Agents and Chemotherapy 57(11): 5398-5405.

Chen, Y.-f., et al. (2011). “Deep sequencing of Cotesia vestalis bracovirus reveals the complexity of a polydnavirus genome.” Virology 414(1): 42-50.

Chen, Y. P., et al. (2013). “Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions.” Bmc Genomics 14.

Chen, Z., et al. (2012). “The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics.” Environmental Microbiology Reports 4(6): 633-641.

Chipman, A. D., et al. (2014). “The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima.” PLoS biology 12(11): e1002005-e1002005.

Cho, N.-H., et al. (2007). “The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes.” Proceedings of the National Academy of Sciences of the United States of America 104(19): 7981-7986.

Choo, S. W., et al. (2012). “Analysis of the Genome of Mycobacterium abscessus Strain M94 Reveals an Uncommon Cluster of tRNAs.” Journal of Bacteriology 194(20): 5724-5724.

Chopin, A., et al. (1999). “Analysis of the Bacillus subtilis genome sequence reveals nine new T-box leaders.” Molecular Microbiology 31(3): 1010-1011.

Chouaia, B., et al. (2014). “Acetic Acid Bacteria Genomes Reveal Functional Traits for Adaptation to Life in Insect Guts.” Genome Biology and Evolution 6(4): 912-920.

Christopherson, M. R., et al. (2013). “The Genome Sequences of Cellulomonas fimi and “Cellvibrio gilvus” Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of “Cellvibrio gilvus” to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp nov.” PLoS ONE 8(1).

Chung, W.-H., et al. (2014). “Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes.” DNA Research 21(2): 153-167.

Cohen-Gihon, I., et al. (2014). “Whole-Genome Sequencing of the Nonproteolytic Bacillus anthracis V770-NP1-R Strain Reveals Multiple Mutations in Peptidase Loci.” Genome announcements 2(1).

Cokus, S. J., et al. (2008). “Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.” Nature 452(7184): 215-219.

Colangeli, R., et al. (2014). “Whole Genome Sequencing of Mycobacterium tuberculosis Reveals Slow Growth and Low Mutation Rates during Latent Infections in Humans.” PLoS ONE 9(3).

Conlan, S., et al. (2012). “Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates.” Genome Biology 13(7).

Conrad, T. M., et al. (2009). “Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.” Genome Biology 10(10).

Creason, A. L., et al. (2014). “Analysis of Genome Sequences from Plant Pathogenic Rhodococcus Reveals Genetic Novelties in Virulence Loci.” PLoS ONE 9(7).

Crossman, L. C., et al. (2008). “The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants.” Genome Biology 9(4).

Cruz-Morales, P., et al. (2013). “The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island.” Genome Biology and Evolution 5(6): 1165-1175.

Cuomo, C. A., et al. (2012). “Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.” Genome Research 22(12): 2478-2488.

Cuomo, C. A., et al. (2007). “The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.” Science 317(5843): 1400-1402.

Curtis, B. A., et al. (2012). “Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.” Nature 492(7427): 59-65.

Darrasse, A., et al. (2013). “Genome sequence of Xanthomonas fuscans subsp fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads.” Bmc Genomics 14.

Dasmahapatra, K. K., et al. (2012). “Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.” Nature 487(7405): 94-98.

de Wit, P. J. G. M., et al. (2012). “The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.” PLoS genetics 8(11).

den Bakker, H. C., et al. (2011). “Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.” Bmc Genomics 12.

Desbiez, C. and H. Lecoq (2004). “The nucleotide sequence of Watermelon mosaic virus (WMV, Potyvirus) reveals interspecific recombination between two related potyviruses in the 5 ‘ part of the genome.” Archives of Virology 149(8): 1619-1632.

Deshpande, N. P., et al. (2011). “Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.” PLoS ONE 6(7): e22170 [22113pp.]-e22170 [22113pp.].

Devi, S. M., et al. (2006). “Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.” Bmc Genomics 7.

Dharia, N. V., et al. (2010). “Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes.” Proceedings of the National Academy of Sciences of the United States of America 107(46): 20045-20050.

Di Genova, A., et al. (2014). “Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants.” Bmc Plant Biology 14.

Dietrich, F. S., et al. (2013). “Genomes of Ashbya Fungi Isolated from Insects Reveal Four Mating-Type Loci, Numerous Translocations, Lack of Transposons, and Distinct Gene Duplications.” G3-Genes Genomes Genetics 3(8): 1225-1239.

Dolores, J. and K. J. F. Satchell (2013). “Analysis of Vibrio cholerae Genome Sequences Reveals Unique rtxA Variants in Environmental Strains and an rtxA-Null Mutation in Recent Altered El Tor Isolates.” Mbio 4(2).

Dorscht, J., et al. (2009). “Comparative Genome Analysis of Listeria Bacteriophages Reveals Extensive Mosaicism, Programmed Translational Frameshifting, and a Novel Prophage Insertion Site.” Journal of Bacteriology 191(23): 7206-7215.

Douillard, F. P., et al. (2013). “Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin.” Microbial Biotechnology 6(5): 576-587.

Drexler, J. F., et al. (2011). “Full genome sequence analysis of parechoviruses from Brazil reveals geographical patterns in the evolution of non-structural genes and intratypic recombination in the capsid region.” Journal of General Virology 92: 564-571.

Du, P., et al. (2011). “A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes.” Bmc Microbiology 11.

Duochun, W., et al. (2011). “Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae.” PLoS ONE 6(6): e21299 [21210pp.]-e21299 [21210pp.].

Duplouy, A., et al. (2013). “Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources.” Bmc Genomics 14.

Dutilh, B. E., et al. (2014). “Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.” Bmc Genomics 15.

Ekman, A., et al. (2009). “Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle.” Bmc Immunology 10.

Elkins, J. G., et al. (2008). “A korarchaeal genome reveals insights into the evolution of the Archaea.” Proceedings of the National Academy of Sciences of the United States of America 105(23): 8102-8107.

Eppinger, M., et al. (2010). “Genome Sequence of the Deep-Rooted Yersinia pestis Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium.” Journal of Bacteriology 192(6): 1685-1699.

Fani, F., et al. (2011). “Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease.” Genome Biology 12(11).

Feng, J., et al. (2008). “Whole Genome Sequencing of Linezolid Resistant Streptococcus pneumoniae Reveal Novel Drug Resistant Mutations.” Abstracts of the Interscience Conference on Antimicrobial Agents and Chemotherapy 48: 181-181.

Feng, J., et al. (2009). “Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance.” Genome Research 19(7): 1214-1223.

Fenn, K. and M. Blaxter (2006). “Wolbachia genomes: revealing the biology of parasitism and mutualism.” Trends in Parasitology 22(2): 60-65.

Fontaine, M. C., et al. (2013). “Complex speciation in the Anopheles gambiae complex revealed by who genome sequencing.” Pathogens and Global Health 107(8): 428-429.

Ford, C., et al. (2012). “Mycobacterium tuberculosis – Heterogeneity revealed through whole genome sequencing.” Tuberculosis 92(3): 194-201.

Fournier, P.-E., et al. (2009). “Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction.” Bmc Genomics 10.

Fouts, D. E., et al. (2013). “Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity.” Virology Journal 10.

Francis, F., et al. (2013). “Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands.” Molecular Genetics and Genomics 288(3-4): 195-203.

Frantz, L. A. F., et al. (2013). “Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus.” Genome Biology 14(9).

Frech, C. and N. Chen (2011). “Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease.” Plos Computational Biology 7(12).

Fricke, W. F., et al. (2006). “The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H-2 for methane formation and ATP synthesis.” Journal of Bacteriology 188(2): 642-658.

Frutos, R., et al. (2006). “Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity.” Journal of Bacteriology 188(7): 2533-2542.

Gagnevin, L., et al. (2013). “Genome and transcriptome analysis to reveal adaptation to new environments and hosts.” Phytopathology 103(6): 170-171.

Galagan, J. E., et al. (2002). “The genome of M-acetivorans reveals extensive metabolic and physiological diversity.” Genome Research 12(4): 532-542.

Gao, S., et al. (2014). “Genome analysis reveals a novel genetically divergent subgenotype of bovine viral diarrhea virus in China.” Infection Genetics and Evolution 21: 489-491.

Garcia, E., et al. (2003). “The genome sequence of Yersinia pestis bacteriophage phi A1122 reveals an intimate history with the coliphage T3 and T7 genomes.” Journal of Bacteriology 185(17): 5248-5262.

Garrigan, D., et al. (2012). “Genome sequencing reveals complex speciation in the Drosophila simulans clade.” Genome Research 22(8): 1499-1511.

Gartemann, K.-H., et al. (2008). “The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp michiganensis NCPPB382 reveals a large island involved in pathogenicity.” Journal of Bacteriology 190(6): 2138-2149.

George, S. G. and M. J. Leaver (2006). “Xenobiotic conjugation in fish: Organisation and diversity of phase 2 genes revealed by genome sequence and EST data.” Marine Environmental Research 62: S54-S55.

Ghedin, E., et al. (2005). “Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.” Nature 437(7062): 1162-1166.

Ghignone, S., et al. (2012). “The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions.” Isme Journal 6(1): 136-145.

Ghosh, S., et al. (2013). “Whole genomic analyses of asymptomatic human G1P 6 , G2P 6 and G3P 6 rotavirus strains reveal intergenogroup reassortment events and genome segments of artiodactyl origin.” Infection Genetics and Evolution 16: 165-173.

Gillece, J. D., et al. (2011). “Whole Genome Sequence Analysis of Cryptococcus gattii from the Pacific Northwest Reveals Unexpected Diversity.” PLoS ONE 6(12).

Ginger, M. L. (2005). “Trypanosomatid biology and euglenozoan evolution: New insights and shifting paradigms revealed through genome sequencing.” Protist 156(4): 377-392.

Godel, C., et al. (2012). “The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets.” Faseb Journal 26(11): 4650-4661.

Gokcumen, O., et al. (2014). “Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.” American Journal of Physical Anthropology 153: 126-127.

Goodhead, I., et al. (2013). “Whole-genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence.” Mbio 4(4).

Goodwin, S. B., et al. (2011). “Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.” PLoS genetics 7(6).

Goodwin, S. B., et al. (2011). “Mycosphaerella comparative genomics reveals chromosome dynamics, genome evolution, and stealth pathogenesis.” Phytopathology 101(6): S208-S208.

Gordon, J. L. and L. D. Sibley (2005). “Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites.” Bmc Genomics 6.

Gou, X., et al. (2014). “Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.” Genome Research 24(8): 1308-1315.

Grbic, M., et al. (2011). “The genome of Tetranychus urticae reveals herbivorous pest adaptations.” Nature 479(7374): 487-492.

Guio, H., et al. (2014). “Genome analysis of 17 extensively drug-resistant strains reveals new potential mutations for resistance.” Genome announcements 2(4).

Guo, X., et al. (2012). “Draft genome sequence of Streptomyces coelicoflavus ZG0656 reveals the putative biosynthetic gene cluster of acarviostatin family a-amylase inhibitors.” Letters in Applied Microbiology 55(2): 162-169.

Guo, X., et al. (2014). “Comparative Genome Analysis Reveals Metabolic Versatility and Environmental Adaptations of Sulfobacillus thermosulfidooxidans Strain ST.” PLoS ONE 9(6).

Gusev, O., et al. (2014). “Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge.” Nature Communications 5.

Guy, L., et al. (2004). “Genomic islands encoded by Staphylococcus aureus chromosomes revealed by genometric analyses.” Abstracts of the Interscience Conference on Antimicrobial Agents and Chemotherapy 44: 62-62.

Hafstrom, T., et al. (2011). “Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.” Bmc Genomics 12.

Halley, Y. A., et al. (2014). “A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene.” PLoS ONE 9(3).

Hammerl, J. A., et al. (2012). “The Complete Genome Sequence of Bacteriophage CP21 Reveals Modular Shuffling in Campylobacter Group II Phages.” Journal of Virology 86(16): 8896-8896.

Han, X., et al. (2011). “Sequence analysis reveals mosaic genome of Aichi virus.” Virology Journal 8.

Hayashida, K., et al. (2012). “Comparative Genome Analysis of Three Eukaryotic Parasites with Differing Abilities To Transform Leukocytes Reveals Key Mediators of Theileria-Induced Leukocyte Transformation.” Mbio 3(5).

Herrero-Medrano, J. M., et al. (2014). “Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.” Bmc Genomics 15.

Hester, J., et al. (2013). “De Novo Assembly of a Field Isolate Genome Reveals Novel Plasmodium vivax Erythrocyte Invasion Genes.” Plos Neglected Tropical Diseases 7(12).

Hiessl, S., et al. (2012). “Involvement of Two Latex-Clearing Proteins during Rubber Degradation and Insights into the Subsequent Degradation Pathway Revealed by the Genome Sequence of Gordonia polyisoprenivorans Strain VH2.” Applied and Environmental Microbiology 78(8): 2874-2887.

Hillier, L. W., et al. (2007). “Comparison of C-elegans and C-briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.” PLoS biology 5(7): 1603-1616.

Ho, T. B. L., et al. (2000). “Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates.” Yeast 17(4): 272-282.

Holmes, E. C., et al. (2005). “Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.” PLoS biology 3(9): 1579-1589.

Hong, J. Y., et al. (2013). “Genetic Aberrations in Imatinib-Resistant Dermatofibrosarcoma Protuberans Revealed by Whole Genome Sequencing.” PLoS ONE 8(7).

Hori, K., et al. (2014). “Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation.” Nature Communications 5.

Hou, S. B., et al. (2004). “Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.” Proceedings of the National Academy of Sciences of the United States of America 101(52): 18036-18041.

Howitt, R. L. J., et al. (2006). “Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant ‘potex-like’ viruses.” Archives of Virology 151(3): 563-579.

Hu, Y. F., et al. (2011). “Complete Genome Analysis of Coxsackievirus A2, A4, A5, and A10 Strains Isolated from Hand, Foot, and Mouth Disease Patients in China Revealing Frequent Recombination of Human Enterovirus A.” Journal of Clinical Microbiology 49(7): 2426-2434.

Hua, W., et al. (2012). “Complete genome sequence of the genotype 4 hepatitis E virus strain prevalent in swine in Jiangsu Province, China, reveals a close relationship with that from the human population in this area.” Journal of Virology 86(15): 8334-8335.

Huang, X., et al. (2012). “A map of rice genome variation reveals the origin of cultivated rice.” Nature 490(7421): 497-+.

Iben, J. R., et al. (2011). “Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants.” Nucleic Acids Research 39(11): 4728-4742.

Ireland, H. S., et al. (2012). “Mining the apple genome reveals a family of nine ethylene receptor genes.” Postharvest Biology and Technology 72: 42-46.

Isaza, J. P., et al. (2012). “Whole genome shotgun sequencing of one Colombian clinical isolate of Mycobacterium tuberculosis reveals DosR regulon gene deletions.” Fems Microbiology Letters 330(2): 113-120.

Izumiya, H., et al. (2011). “Whole-Genome Analysis of Salmonella enterica Serovar Typhimurium T000240 Reveals the Acquisition of a Genomic Island Involved in Multidrug Resistance via IS1 Derivatives on the Chromosome.” Antimicrobial Agents and Chemotherapy 55(2): 623-630.

Jack, P. J. M., et al. (2005). “The complete genome sequence of J virus reveals a unique genome structure in the family Paramyxoviridae.” Journal of Virology 79(16): 10690-10700.

James, D., et al. (2014). “Analysis of the complete genome of a virus associated with twisted leaf disease of cherry reveals evidence of a close relationship to unassigned viruses in the family Betaflexiviridae.” Archives of Virology 159(9): 2463-2468.

James, T. Y., et al. (2013). “Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems.” Mycologia 105(6): 1374-1390.

Janbon, G., et al. (2014). “Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation.” PLoS genetics 10(4).

Janto, B., et al. (2011). “Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4.” Environmental Microbiology 13(12): 3289-3309.

Jere, K. C., et al. (2012). “Whole genome sequence analyses of three African bovine rotaviruses reveal that they emerged through multiple reassortment events between rotaviruses from different mammalian species.” Veterinary Microbiology 159(1–2): 245-250.

Jere, K. C., et al. (2011). “Whole genome analysis of multiple rotavirus strains from a single stool specimen using sequence-independent amplification and 454 (R) pyrosequencing reveals evidence of intergenotype genome segment recombination.” Infection Genetics and Evolution 11(8): 2072-2082.

Jia, J., et al. (2013). “Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.” Nature 496(7443): 91-95.

Jiao, N., et al. (2010). “Coexistence of Two Different Photosynthetic Operons in Citromicrobium bathyomarinum JL354 As Revealed by Whole-Genome Sequencing.” Journal of Bacteriology 192(4): 1169-1170.

Jones, N. C. and P. A. Pevzner (2006). “Comparative genomics reveals unusually long motifs in mammalian genomes.” Bioinformatics 22(14): E236-E242.

Joshi, M. N., et al. (2013). “Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation.” Genome announcements 1(4).

Jung, S., et al. (2012). “Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.” Bmc Genomics 13.

Kaakoush, N. O., et al. (2011). “Comparative analyses of Campylobacter concisus strains reveal the genome of the reference strain BAA-1457 is not representative of the species.” Gut Pathogens 3.

Kasimatis, G., et al. (2013). “Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain.” BioMed research international 2013: 918320-918320.

Khamrin, P., et al. (2013). “Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.” Infection Genetics and Evolution 17: 132-136.

Khamrin, P., et al. (2013). “Complete genome sequence of human bocavirus 4 reveals genetic diversity of coding sequences.” International Journal of Antimicrobial Agents 42: S135-S135.

Kim, E. B., et al. (2011). “Genome sequencing reveals insights into physiology and longevity of the naked mole rat.” Nature 479(7372): 223-227.

Kim, J. M., et al. (1998). “Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence.” Genome Research 8(5): 464-478.

Kim, N.-H., et al. (2014). “Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag-simple sequence repeat bands in Panax ginseng Meyer.” Journal of Ginseng Research 38(2): 130-135.

Kimbrel, J. A., et al. (2013). “The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.” Genome announcements 1(4).

Knetsch, C., et al. (2014). “Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011.” Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 19(45).

Koo, H., et al. (2014). “Draft Genome Sequence of Hymenobacter sp. Strain IS2118, Isolated from a Freshwater Lake in Schirmacher Oasis, Antarctica, Reveals Diverse Genes for Adaptation to Cold Ecosystems.” Genome announcements 2(4).

Kosaka, T., et al. (2008). “The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota.” Genome Research 18(3): 442-448.

Kosaraju, P., et al. (2005). “Analysis of the genome of Azotobacter vinelandii revealed the presence of two genetically distinct group II introns on the chromosome.” Genetica 124(2-3): 107-115.

Kovacs, G. M., et al. (2004). “Analysis of the first complete genome sequence of an Old World monkey adenovirus reveals a lineage distinct from the six human adenovirus species.” Journal of General Virology 85: 2799-2807.

Kramvis, A., et al. (2005). “Full genome analysis of hepatitis B virus genotype E strains from south-western Africa and Madagascar reveals low genetic variability.” Journal of Medical Virology 77(1): 47-52.

Krueger, E. N., et al. (2013). “The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses.” Frontiers in Microbiology 4.

Kumar, M. and P. V. Balaji (2011). “Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes.” Molecular Biosystems 7(5): 1629-1645.

Kumar, S., et al. (2008). “Complete genome sequence of avian paramyxovirus type 3 reveals an unusually long trailer region.” Virus Research 137(2): 189-197.

Kurath, G., et al. (2004). “Complete genome sequence of Fer-de-Lance virus reveals a novel gene in reptilian paramyxoviruses.” Journal of Virology 78(4): 2045-2056.

Kuroda, M., et al. (2005). “Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection.” Proceedings of the National Academy of Sciences of the United States of America 102(37): 13272-13277.

Kvitek, D. J. and G. Sherlock (2013). “Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment.” PLoS genetics 9(11).

Labonte, J. M. and C. A. Suttle (2013). “Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea.” Frontiers in Microbiology 4.

Labrie, S. J., et al. (2013). “Genomes of marine cyanopodoviruses reveal multiple origins of diversity.” Environmental Microbiology 15(5): 1356-1376.

Lamour, K. H., et al. (2012). “Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici.” Molecular Plant-Microbe Interactions 25(10): 1350-1360.

Lane, C. E., et al. (2007). “Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function.” Proceedings of the National Academy of Sciences of the United States of America 104(50): 19908-19913.

Lapidus, A., et al. (2011). “Genomes of Three Methylotrophs from a Single Niche Reveal the Genetic and Metabolic Divergence of the Methylophilaceae.” Journal of Bacteriology 193(15): 3757-3764.

Lauer, P., et al. (2005). “Genome analysis reveals pili in group B Streptococcus.” Science 309(5731): 105-105.

Laurie, J. D., et al. (2012). “Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements.” Plant Cell 24(5): 1733-1745.

Lee, H. S., et al. (2008). “The Complete Genome Sequence of Thermococcus onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism.” Journal of Bacteriology 190(22): 7491-7499.

Lehours, P., et al. (2011). “Genome Sequencing Reveals a Phage in Helicobacter pylori.” Mbio 2(6).

Lemos, B. (2007). “The Opossum genome reveals further evidence for regulatory evolution in mammalian diversification.” Genome Biology 8(8).

Lenassi, M., et al. (2013). “Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii.” PLoS ONE 8(8).

Levesque, C. A., et al. (2010). “Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.” Genome Biology 11(7).

Li, T., et al. (2013). “Exploring the apple genome reveals six ACC synthase genes expressed during fruit ripening.” Scientia Horticulturae 157: 119-123.

Li, X., et al. (2013). “Comparative genome characterization of Achromobacter members reveals potential genetic determinants facilitating the adaptation to a pathogenic lifestyle.” Applied Microbiology and Biotechnology 97(14): 6413-6425.

Li, Y.-h., et al. (2013). “Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.” Bmc Genomics 14.

Libants, S., et al. (2009). “The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage.” BMC Evolutionary Biology 9: 14pp.-14pp.

Lin, K., et al. (2014). “Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus.” PLoS genetics 10(1).

Links, M. G., et al. (2011). “De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes.” Bmc Genomics 12.

Liu, S., et al. (2014). “The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.” Nature Communications 5.

Liu, X., et al. (2013). “Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome.” Infection Genetics and Evolution 14: 29-38.

Lorenzi, H. A., et al. (2010). “New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information.” Plos Neglected Tropical Diseases 4(6).

Lowe, C. B. and D. Haussler (2012). “29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome.” PLoS ONE 7(8).

Lu, L., et al. (2014). “Full-length genomes of 16 hepatitis C virus genotype 1 isolates representing subtypes 1c, 1d, 1e, 1g, 1h, 1i, 1j and 1k, and two new subtypes 1m and 1n, and four unclassified variants reveal ancestral relationships among subtypes.” Journal of General Virology 95: 1479-1487.

Luthra, P. M. and R. Luthra (2003). “Sequencing of the malarial parasite genome reveals potential drug targets to combat malaria.” Current Science 84(5): 623-625.

Lynch, E. A., et al. (2012). “Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux.” PLoS ONE 7(7).

Ma, J. and Y.-B. Shi (2014). “The Mesobuthus martensii genome reveals the molecular diversity of scorpion toxins.” Cell and Bioscience 4.

Ma, Y.-F., et al. (2009). “The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments.” Applied and Environmental Microbiology 75(21): 6812-6819.

Mace, E. S. and D. R. Jordan (2011). “Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.” Theoretical and Applied Genetics 123(1): 169-191.

Mace, E. S., et al. (2013). “Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum.” Nature Communications 4.

Maeder, D. L., et al. (2006). “The Methanosarcina barkeri genome: Comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes.” Journal of Bacteriology 188(22): 7922-7931.

Malaspinas, A.-S., et al. (2014). “Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.” Current Biology 24(21): R1035-R1037.

Manfredi, P., et al. (2011). “The genome and surface proteome of Capnocytophaga canimorsus reveal a key role of glycan foraging systems in host glycoproteins deglycosylation.” Molecular Microbiology 81(4): 1050-1060.

Mann, A. J., et al. (2013). “The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901(T) Reveals a Broad Potential for Degradation of Algal Polysaccharides.” Applied and Environmental Microbiology 79(21): 6813-6822.

Marathe, N. P., et al. (2014). “Genome sequencing of multidrug resistant novel Clostridium sp BL8 reveals its potential for pathogenicity.” Gut Pathogens 6.

Marcelletti, S., et al. (2011). “Pseudomonas syringae pv. actinidiae Draft Genomes Comparison Reveal Strain-Specific Features Involved in Adaptation and Virulence to Actinidia Species.” PLoS ONE 6(11).

Marri, P. R., et al. (2010). “Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species.” PLoS ONE 5(7).

Martinez, D. A., et al. (2012). “Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection.” Mbio 3(5).

Martinez, M., et al. (2014). “Whole-genome analyses reveals the animal origin of a rotavirus G4P 6 detected in a child with severe diarrhea.” Infection Genetics and Evolution 27: 156-162.

Marvig, R. L., et al. (2013). “Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators.” PLoS genetics 9(9).

Matthijnssens, J., et al. (2012). “Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation.” Journal of General Virology 93: 866-875.

Mattupalli, C., et al. (2014). “A Draft Genome Sequence Reveals the Helminthosporium solani Arsenal for Cell Wall Degradation.” American Journal of Potato Research 91(5): 517-524.

Mavromatis, K., et al. (2006). “The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies.” Journal of Bacteriology 188(11): 4015-4023.

McBride, C. S. and J. R. Arguello (2007. “Five Drosophila Genomes Reveal Nonneutral Evolution and the Signature of Host Specialization in the Chemoreceptor Superfamily.” Genetics 177: 1395.

McBride, M. J., et al. (2009). “Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis.” Applied and Environmental Microbiology 75(21): 6864-6875.

McDowell, J. M. (2011). “Genomes of obligate plant pathogens reveal adaptations for obligate parasitism.” Proceedings of the National Academy of Sciences of the United States of America 108(22): 8921-8922.

McGaugh, S. E., et al. (2014). “The cavefish genome reveals candidate genes for eye loss.” Nature Communications 5.

McIlroy, S. J., et al. (2014). “‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity.” Isme Journal 8(3): 613-624.

McTaggart, S. J., et al. (2009). “The components of the Daphnia pulex immune system as revealed by complete genome sequencing.” Bmc Genomics 10.

Meczker, K., et al. (2014). “The genome of the Erwinia amylovora phage PhiEaH1 reveals greater diversity and broadens the applicability of phages for the treatment of fire blight.” Fems Microbiology Letters 350(1): 25-27.

Meier, B., et al. (2014). “C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency.” Genome Research 24(10): 1624-1636.

Mejean, A., et al. (2010). “The Genome Sequence of the Cyanobacterium Oscillatoria sp. PCC 6506 Reveals Several Gene Clusters Responsible for the Biosynthesis of Toxins and Secondary Metabolites.” Journal of Bacteriology 192(19): 5264-5265.

Menard, D., et al. (2013). “Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains.” Plos Neglected Tropical Diseases 7(11).

Meng, B. Z., et al. (1998). “Nucleotide sequence and genome structure of grapevine rupestris stem pitting associated virus-1 reveal similarities to apple stem pitting virus.” Journal of General Virology 79: 2059-2069.

Mercer, A. A., et al. (2006). “Comparative analysis of genome sequences of three isolates of Orf virus reveals unexpected sequence variation.” Virus Research 116(1-2): 146-158.

Merchant, S. S., et al. (2007). “The Chlamydomonas genome reveals the evolution of key animal and plant functions.” Science (Washington D C) 318(5848): 245-251.

Merker, M., et al. (2013). “Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients.” PLoS ONE 8(12).

Methe, B. A., et al. (2005). “The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.” Proceedings of the National Academy of Sciences of the United States of America 102(31): 10913-10918.

Middleton, C. P., et al. (2013). “Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity.” Plant Journal 73(2): 347-356.

Mikkelsen, T. S., et al. (2007). “Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.” Nature 447(7141): 167-U161.

Miller, W., et al. (2012). “Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.” Proceedings of the National Academy of Sciences of the United States of America 109(36): E2382-E2390.

Mitter, B., et al. (2013). “Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants.” Frontiers in Plant Science 4.

Mongodin, E. F., et al. (2006). “Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.” PLoS genetics 2(12): 2094-2106.

Moore, C. E., et al. (2012). “Nucleomorph Genome Sequence of the Cryptophyte Alga Chroomonas mesostigmatica CCMP1168 Reveals Lineage-Specific Gene Loss and Genome Complexity.” Genome Biology and Evolution 4(11): 1162-1175.

Moran, M. A., et al. (2004). “Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.” Nature 432(7019): 910-913.

Moran, Y., et al. (2008). “Concerted evolution of sea anemone neurotoxin genes is revealed through analysis of the Nematostella vectensis genome.” Molecular Biology and Evolution 25(4): 737-747.

Morin, E., et al. (2012). “Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.” Proceedings of the National Academy of Sciences of the United States of America 109(43): 17501-17506.

Morita, H., et al. (2008). “Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production.” DNA Research 15(3): 151-161.

Moss, S. P., et al. (2011). “Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage.” Genome Biology and Evolution 3: 1187-1196.

Moura, A. E., et al. (2014). “Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum.” Molecular Biology and Evolution 31(5): 1121-1131.

Mourier, T., et al. (2001). “The human genome project reveals a continuous, transfer of large mitochondrial fragments to the nucleus.” Molecular Biology and Evolution 18(9): 1833-1837.

Mwangi, M. M., et al. (2013). “Whole-Genome Sequencing Reveals a Link Between beta-Lactam Resistance and Synthetases of the Alarmone (p)ppGpp in Staphylococcus aureus.” Microbial Drug Resistance 19(3): 153-159.

Naito, M., et al. (2008). “Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P-gingivalis.” DNA Research 15(4): 215-225.

Nakagawa, I., et al. (2003). “Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution.” Genome Research 13(6): 1042-1055.

Nakayama, K., et al. (2008). “The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During Reductive Genome Evolution.” DNA Research 15(4): 185-199.

Nakayama, T., et al. (2014). “Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.” Proceedings of the National Academy of Sciences of the United States of America 111(31): 11407-11412.

Nakazawa, H., et al. (2009). “Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria.” Genome Research 19(10): 1801-1808.

Nelson, K. E., et al. (2004). “Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.” Nucleic Acids Research 32(8): 2386-2395.

Ng, V. and W.-J. Lin (2014). “Comparison of assembled Clostridium botulinum A1 genomes revealed their evolutionary relationship.” Genomics 103(1): 94-106.

Nie, Y., et al. (2013). “The Genome of the Moderate Halophile Amycolicicoccus subflavus DQS3-9A1(T) Reveals Four Alkane Hydroxylation Systems and Provides Some Clues on the Genetic Basis for Its Adaptation to a Petroleum Environment.” PLoS ONE 8(8).

Nie, Y., et al. (2012). “The Genome Sequence of Polymorphum gilvum SL003B-26A1(T) Reveals Its Genetic Basis for Crude Oil Degradation and Adaptation to the Saline Soil.” PLoS ONE 7(2).

Nikaido, M., et al. (2013). “Coelacanth genomes reveal signatures for evolutionary transition from water to land.” Genome Research 23(10): 1740-1748.

Niskanen, E. A., et al. (2005). “Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family.” Bmc Genomics 6.

Noonan, J. P., et al. (2004). “Coelacanth genome sequence reveals the evolutionary history of vertebrate genes.” Genome Research 14(12): 2397-2405.

Nossa, C. W., et al. (2014). “Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication.” GigaScience 3: 9-9.

Novichkov, P. S., et al. (2009). “Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes.” Journal of Bacteriology 191(1): 65-73.

Novo, C., et al. (2003). “Burkholderia genome analysis reveals new enzymes belonging to the nitrilase superfamily – The amidase of Burkholderia cepacia (hospital isolate).” International Journal of Biological Macromolecules 33(4-5): 175-182.

Novo, M., et al. (2009). “Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118.” Proceedings of the National Academy of Sciences of the United States of America 106(38): 16333-16338.

Nunoura, T., et al. (2011). “Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.” Nucleic Acids Research 39(8): 3204-3223.

Oda, Y., et al. (2008). “Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments.” Proceedings of the National Academy of Sciences of the United States of America 105(47): 18543-18548.

Ogawa, Y., et al. (2011). “The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism’s Intracellular Adaptations.” Journal of Bacteriology 193(12): 2959-2971.

Okamura, Y., et al. (2005). “Comprehensive analysis of the ascidian genome reveals novel insights into the molecular evolution of ion channel genes.” Physiological Genomics 22(3): 269-282.

O’Neill, C. E., et al. (2013). “Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.” Microbiology-Sgm 159: 748-756.

Ong, H. S., et al. (2012). “Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp.” Comparative and Functional Genomics 2012: 752867-752867.

Opperman, C. H., et al. (2010). “Plant-parasitic nematode genomes: comparative analysis begins to reveal paths to adaptation and evolution.” Journal of Nematology 42(3): 261-261.

Osterman, J., et al. (2014). “Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors.” Bmc Genomics 15.

Otto, T. D., et al. (2014). “Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.” Nature Communications 5.

Padamsee, M., et al. (2012). “The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction.” Fungal Genetics and Biology 49(3): 217-226.

Palmeira, L., et al. (2011). “Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features.” Virology Journal 8.

Palmenberg, A. C., et al. (2009). “Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveal Structure and Evolution.” Science 324(5923): 55-59.

Pan, G., et al. (2013). “Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation.” Bmc Genomics 14.

Pan, K., et al. (2011). “Nuclear monophyly and asexual propagation of Nannochloropsis oceanica (Eustigmatophyceae) as revealed by its genome sequence.” Journal of Phycology 47(6): 1425-1432.

Pareek, A., et al. (2006). “Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with arabidopsis.” Plant Physiology 142(2): 380-397.

Park, Y.-J., et al. (2014). “Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation.” PLoS ONE 9(4).

Parkhill, J., et al. (2000). “The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.” Nature 403(6770): 665-668.

Parvin, R., et al. (2014). “Full-genome analysis of avian influenza virus H9N2 from Bangladesh reveals internal gene reassortments with two distinct highly pathogenic avian influenza viruses.” Archives of Virology 159(7): 1651-1661.

Pearson, M. D. and H. F. Noller (2011). “The Draft Genome of Planococcus donghaensis MPA1U2 Reveals Nonsporulation Pathways Controlled by a Conserved Spo0A Regulon.” Journal of Bacteriology 193(21): 6106-6106.

Pei, C., et al. (2014). “Complete genome sequence and comparative analysis of grass carp reovirus strain 109 (GCReV-109) with other grass carp reovirus strains reveals no significant correlation with regional distribution.” Archives of Virology 159(9): 2435-2440.

Penz, T., et al. (2010). “The genome of the amoeba symbiont “Candidatus Amoebophilus asiaticus” reveals common mechanisms for host cell interaction among amoeba-associated bacteria.” Virulence 1(6): 541-545.

Pepin, K. M. and H. A. Wichman (2008). “Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage phi X174.” BMC Evolutionary Biology 8.

Pereira Ramos, P. I., et al. (2014). “Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms.” Bmc Genomics 15.

Petty, N. K., et al. (2010). “The Citrobacter rodentium Genome Sequence Reveals Convergent Evolution with Human Pathogenic Escherichia coli.” Journal of Bacteriology 192(2): 525-538.

Piet, J. R., et al. (2010). “Whole Pneumococcal Genome Sequencing in a Clinical-Based Approach Reveals Novel Factors Associated with Less Severe Disease in Meningitis.” Abstracts of the Interscience Conference on Antimicrobial Agents and Chemotherapy 50.

Pombert, J.-F., et al. (2013). “Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi.” Eukaryotic Cell 12(4): 503-511.

Porcel, B. M., et al. (2014). “The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants.” PLoS genetics 10(2): e1004007-e1004007.

Pourkarim, M. R., et al. (2009). “Evolutionary analysis of Hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium.” Journal of Clinical Virology 46: S8-S8.

Power, P. M., et al. (2004). “Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli.” Biochemical and Biophysical Research Communications 322(3): 1038-1044.

Prado-Martinez, J., et al. (2013). “The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.” Bmc Genomics 14.

Procopio, L., et al. (2012). “Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential.” Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 101(2): 289-302.

Putnam, N. H., et al. (2007). “Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.” Science 317(5834): 86-94.

Qin, Q.-L., et al. (2010). “The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.” Bmc Genomics 11.

Qiu, J., et al. (2014). “Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.” PLoS ONE 9(9): e108479-e108479.

Qiu, X., et al. (2011). “Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size.” Virology Journal 8.

Qu, Y., et al. (2013). “Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.” Nature Communications 4.

Raffaele, S., et al. (2010). “Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans.” Bmc Genomics 11.

Raghavan, M., et al. (2014). “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.” Nature 505(7481): 87-+.

Rasko, D. A., et al. (2004). “The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.” Nucleic Acids Research 32(3): 977-988.

Rasmussen, M., et al. (2011). “An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia.” Science 334(6052): 94-98.

Rauschenbach, I., et al. (2011). “Energy metabolism and multiple respiratory pathways revealed by genome sequencing of Desulfurispirillum indicum strain S5.” Environmental Microbiology 13(6): 1611-1621.

Read, T. D., et al. (2013). “Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range.” Mbio 4(2).

Redondo-Nieto, M., et al. (2013). “Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction.” Bmc Genomics 14.

Remenant, B., et al. (2010). “Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence.” Bmc Genomics 11.

Ren, S. X., et al. (2003). “Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing.” Nature 422(6934): 888-893.

Renny-Byfield, S., et al. (2011). “Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs.” Molecular Biology and Evolution 28(10): 2843-2854.

Rensing, S. A., et al. (2008). “The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.” Science 319(5859): 64-69.

Renzoni, A., et al. (2011). “Whole Genome Sequencing and Complete Genetic Analysis Reveals Novel Pathways to Glycopeptide Resistance in Staphylococcus aureus.” PLoS ONE 6(6).

Rich, S. M. (2004). “The unpredictable past of Plasmodium vivax revealed in its genome.” Proceedings of the National Academy of Sciences of the United States of America 101(44): 15547-15548.

Richter, M., et al. (2007). “Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.” Journal of Bacteriology 189(13): 4899-4910.

Ride, J. P., et al. (1999). “Analysis of Arabidopsis genome sequence reveals a large new gene family in plants.” Plant Molecular Biology 39(5): 927-932.

Robinson, R. (2006). “Ciliate genome sequence reveals unique features of a model eukaryote.” PLoS biology 4(9): e304-e304.

Rodriguez-Palenzuela, P., et al. (2010). “Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts.” Environmental Microbiology 12(6): 1604-1620.

Rondeau, E. B., et al. (2014). “The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei.” PLoS ONE 9(7).

Rosenblum, E. B., et al. (2013). “Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data.” Proceedings of the National Academy of Sciences of the United States of America 110(23): 9385-9390.

Roy, A. and R. H. Brlansky (2010). “Genome analysis of an orange stem pitting citrus tristeza virus isolate reveals a novel recombinant genotype.” Virus Research 151(2): 118-130.

Roy, A., et al. (2011). “Genome sequence of an unassigned Citrus tristeza virus genotypic isolate from Puerto Rico reveals a trifoliate resistance breaking genotype.” Phytopathology 101(6): S156-S156.

Roy, A., et al. (2013). “Genome assembly of citrus leprosis virus nuclear type reveals a close association with orchid fleck virus.” Genome announcements 1(4).

Rubin, C.-J., et al. (2010). “Whole-genome resequencing reveals loci under selection during chicken domestication.” Nature 464(7288): 587-U145.

Rueckert, C., et al. (2011). “Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42.” Journal of Biotechnology 155(1): 78-85.

Rychli, K., et al. (2014). “Genome sequencing of Listeria monocytogenes “Quargel” listeriosis outbreak strains reveals two different strains with distinct in vitro virulence potential.” PLoS ONE 9(2): e89964 [89911pp.]-e89964 [89911pp.].

Safina, N. P., et al. (2014). “Whole genome sequencing in male siblings with Burn-McKeown Syndrome reveals MAP3K15 as a novel disease gene candidate.” American Journal of Medical Genetics Part A 164A(8): 1887-1887.

Sailaja, B., et al. (2013). “The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.” Virus Genes 47(3): 515-523.

Samuel, A. S., et al. (2010). “Complete Genome Sequence of Avian Paramyxovirus (APMV) Serotype 5 Completes the Analysis of Nine APMV Serotypes and Reveals the Longest APMV Genome.” PLoS ONE 5(2).

Sangal, V., et al. (2012). “The Draft Genome Sequence of Corynebacterium diphtheriae bv. mitis NCTC 3529 Reveals Significant Diversity between the Primary Disease-Causing Biovars.” Journal of Bacteriology 194(12): 3269-3269.

Sarkar, T., et al. (2014). “Whole Genome Sequencing Reveals Novel Non-Synonymous Mutation in Ectodysplasin A (EDA) Associated with Non-Syndromic X-Linked Dominant Congenital Tooth Agenesis.” PLoS ONE 9(9).

Saxer, G., et al. (2012). “Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum.” PLoS ONE 7(10).

Schardl, C. L., et al. (2013). “Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci.” PLoS genetics 9(2).

Schiffer, P. H., et al. (2013). “The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda.” Bmc Genomics 14.

Schirawski, J., et al. (2010). “Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison.” Science 330(6010): 1546-1548.

Schistosoma japonicum Genome, S., et al. (2009). “The Schistosoma japonicum genome reveals features of host-parasite interplay.” Nature 460(7253): 345-351.

Schmitz-Esser, S., et al. (2010). “The Genome of the Amoeba Symbiont “Candidatus Amoebophilus asiaticus” Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria.” Journal of Bacteriology 192(4): 1045-1057.

Schneider, J., et al. (2012). “Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities.” FEMS Yeast Research 12(3): 382-386.

Schreiber, M., et al. (2014). “The Barley Genome Sequence Assembly Reveals Three Additional Members of the CslF (1,3;1,4)-beta-Glucan Synthase Gene Family.” PLoS ONE 9(3).

Sczesnak, A., et al. (2011). “The Genome of Th17 Cell-Inducing Segmented Filamentous Bacteria Reveals Extensive Auxotrophy and Adaptations to the Intestinal Environment.” Cell Host & Microbe 10(3): 260-272.

Sebaihia, M., et al. (2006). “Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B-bronchiseptica, B-pertussis, and B-parapertussis reveals extensive diversity in surface structures associated with host interaction.” Journal of Bacteriology 188(16): 6002-6015.

Seim, I., et al. (2013). “Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii.” Nature Communications 4.

Sela, D. A., et al. (2008). “The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome.” Proceedings of the National Academy of Sciences of the United States of America 105(48): 18964-18969.

Semeiks, J., et al. (2014). “Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys.” Bmc Genomics 15.

Serviene, E., et al. (2012). “Screening the Budding Yeast Genome Reveals Unique Factors Affecting K2 Toxin Susceptibility.” PLoS ONE 7(12).

Shetty, S. A., et al. (2013). “Comparative Genome Analysis of Megasphaera sp Reveals Niche Specialization and Its Potential Role in the Human Gut.” PLoS ONE 8(11).

Shi, X., et al. (2012). “Genome Sequence of the Thermostable-Agarase-Producing Marine Bacterium Catenovulum agarivorans YM01(T), Which Reveals the Presence of a Series of Agarase-Encoding Genes.” Journal of Bacteriology 194(19): 5484-5484.

Shoguchi, E., et al. (2013). “Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure.” Current Biology 23(15): 1399-1408.

Silva, J. C., et al. (2011). “Genome sequences reveal divergence times of malaria parasite lineages.” Parasitology 138(13): 1737-1749.

Singh, R., et al. (2013). “Oil palm genome sequence reveals divergence of interfertile species in Old and New Worlds.” Nature 500(7462): 335-+.

Sirota-Madi, A., et al. (2010). “Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.” Bmc Genomics 11.

Sivaraman, K., et al. (2008). “Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage.” Bmc Genomics 9.

Sjodin, A., et al. (2010). “Whole-Genome Sequencing Reveals Distinct Mutational Patterns in Closely Related Laboratory and Naturally Propagated Francisella tularensis Strains.” PLoS ONE 5(7).

Sjodin, A., et al. (2012). “Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish.” Bmc Genomics 13.

Smith, S. R., et al. (2012). “Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways.” Algal Research-Biomass Biofuels and Bioproducts 1(1): 2-16.

Soanes, D. M., et al. (2008). “Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis.” PLoS ONE 3(6).

Song, L., et al. (2013). “Genetic variability of mutans streptococci revealed by wide whole-genome sequencing.” Bmc Genomics 14.

Song, Y., et al. (2013). “Additional Routes to Staphylococcus aureus Daptomycin Resistance as Revealed by Comparative Genome Sequencing, Transcriptional Profiling, and Phenotypic Studies.” PLoS ONE 8(3).

Soria-Carrasco, V., et al. (2014). “Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation.” Science 344(6185): 738-742.

Souter, A., et al. (2000). “The genome sequence of Mycobacterium tuberculosis reveals cytochromes P450 as novel anti-TB drug targets.” Journal of Chemical Technology and Biotechnology 75(10): 933-941.

Souvik, G., et al. (2011). “Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P 4 human rotavirus strains.” Journal of General Virology 92(9): 2201-2208.

Spring, S., et al. (2010). “The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments.” Archaea-an International Microbiological Journal.

Staats, C. C., et al. (2014). “Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins.” Bmc Genomics 15.

Stanley, D. N., et al. (2013). “Comparative Analysis of 126 Cyanobacterial Genomes Reveals Evidence of Functional Diversity Among Homologs of the Redox-Regulated CP12 Protein.” Plant Physiology 161(2): 824-835.

Star, B., et al. (2011). “The genome sequence of Atlantic cod reveals a unique immune system.” Nature 477(7363): 207-210.

Starkenburg, S. R., et al. (2014). “A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes.” Bmc Genomics 15.

Storm, M., et al. (2007). “Comparison of two Lactobacillus reuteri genomes reveal divergence within a probiotic species.” Abstracts of the General Meeting of the American Society for Microbiology 107: 505-505.

Studholme, D. J., et al. (2009). “A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528.” Bmc Genomics 10.

Studholme, D. J., et al. (2011). “Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.” Genes 2(4): 1050-1065.

Su, H.-C., et al. (2013). “Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development.” Microbial Drug Resistance 19(6): 428-436.

Suen, G., et al. (2011). “The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle.” PLoS genetics 7(2).

Suen, G., et al. (2011). “The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist.” PLoS ONE 6(4).

Suga, H., et al. (2013). “The Capsaspora genome reveals a complex unicellular prehistory of animals.” Nature Communications 4.

Suh, A., et al. (2013). “The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses.” Nature Communications 4.

Sullivan, N. L., et al. (2013). “The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain.” Genome announcements 1(5).

Sun, G., et al. (2012). “Complete Genome Sequence of a Novel Type of Human Parechovirus Strain Reveals Natural Recombination Events.” Journal of Virology 86(16): 8892-8893.

Suzuki, M., et al. (2009). “Analysis of Nucleotide Sequences of Human Parvovirus B19 Genome Reveals Two Different Modes of Evolution, a Gradual Alteration and a Sudden Replacement: a Retrospective Study in Sapporo, Japan, from 1980 to 2008.” Journal of Virology 83(21): 10975-10980.

Swingley, W. D., et al. (2007). “The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.” Journal of Bacteriology 189(3): 683-690.

Takaki, Y., et al. (2010). “Bacterial Lifestyle in a Deep-sea Hydrothermal Vent Chimney Revealed by the Genome Sequence of the Thermophilic Bacterium Deferribacter desulfuricans SSM1.” DNA Research 17(3): 123-137.

Takami, H., et al. (2004). “Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus.” Nucleic Acids Research 32(21): 6292-6303.

Takeuchi, K., et al. (2014). “Complete Genome Sequence of the Biocontrol Strain Pseudomonas protegens Cab57 Discovered in Japan Reveals Strain-Specific Diversity of This Species.” PLoS ONE 9(4).

Tang, H., et al. (2010). “Angiosperm genome comparisons reveal early polyploidy in the monocot lineage.” Proceedings of the National Academy of Sciences of the United States of America 107(1): 472-477.

Tanifuji, G., et al. (2011). “Complete Nucleomorph Genome Sequence of the Nonphotosynthetic Alga Cryptomonas paramecium Reveals a Core Nucleomorph Gene Set.” Genome Biology and Evolution 3: 44-54.

Thieme, F., et al. (2005). “Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.” Journal of Bacteriology 187(21): 7254-7266.

Thole, S., et al. (2012). “Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life.” Isme Journal 6(12): 2229-2244.

Thomas, T., et al. (2008). “Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment.” PLoS ONE 3(9).

Thomson, N. R., et al. (2005). “The Chlamlydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.” Genome Research 15(5): 629-640.

Tian, M., et al. (2011). “454 Genome Sequencing of Pseudoperonospora cubensis Reveals Effector Proteins with a QXLR Translocation Motif.” Molecular Plant-Microbe Interactions 24(5): 543-553.

Tomida, S., et al. (2013). “Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome.” Mbio 4(3).

Toome, M., et al. (2013). “The genome of the fern pathogen Mixia osmundae reveals hints about its cryptic biology.” Phytopathology 103(6): 146-146.

Torriani, S. F. F., et al. (2014). “Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion.” Fungal Genetics and Biology 62: 34-42.

Trost, E., et al. (2010). “The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.” Bmc Genomics 11.

Tsai, I. J., et al. (2013). “The genomes of four tapeworm species reveal adaptations to parasitism.” Nature 496(7443): 57-63.

Tsipouri, V., et al. (2008). “Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome.” Genome Biology 9(10).

Tsugawa, T. and Y. Hoshino (2008). “Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P 3 strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans.” Virology 380(2): 344-353.

Tsuru, T. and I. Kobayashi (2008). “Intra-specific multiple genome comparison in Staphylococcus aureus reveals a unit of evolution spanning two adjacent genes in a tandem paralogue cluster.” Genes & Genetic Systems 83(6): 518-518.

Turajlic, S., et al. (2014). “Whole-genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition.” Annals of Oncology 25(5): 959-967.

Turner, P. C., et al. (2012). “Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes.” Journal of Industrial Microbiology & Biotechnology 39(4): 629-639.

Turroni, F., et al. (2010). “Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.” Proceedings of the National Academy of Sciences of the United States of America 107(45): 19514-19519.

Twito, T., et al. (2011). “Comparative genome analysis with the human genome reveals chicken genes associated with fatness and body weight.” Animal Genetics 42(6): 642-649.

Uchiya, K.-i., et al. (2013). “Comparative Genome Analysis of Mycobacterium avium Revealed Genetic Diversity in Strains that Cause Pulmonary and Disseminated Disease.” PLoS ONE 8(8).

Udpa, N., et al. (2014). “Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes.” Genome Biology 15(2).

Udwary, D. W., et al. (2007). “Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica.” Proceedings of the National Academy of Sciences of the United States of America 104(25): 10376-10381.

van de Guchte, M., et al. (2006). “The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.” Proceedings of the National Academy of Sciences of the United States of America 103(24): 9274-9279.

Vandroemme, J., et al. (2013). “Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content.” Bmc Genomics 14.

Ventura, M., et al. (2011). “Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.” Genome Research 21(10): 1640-1649.

Vera-Cabrera, L., et al. (2013). “Complete Genome Sequence Analysis of Nocardia brasiliensis HUJEG-1 Reveals a Saprobic Lifestyle and the Genes Needed for Human Pathogenesis.” PLoS ONE 8(6).

Vieira, F. G., et al. (2012). “Unique Features of Odorant-Binding Proteins of the Parasitoid Wasp Nasonia vitripennis Revealed by Genome Annotation and Comparative Analyses.” PLoS ONE 7(8).

Voloch, C. M., et al. (2014). “Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification.” Viruses 6(11): 4465-4478.

Vonk, F. J., et al. (2013). “The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.” Proceedings of the National Academy of Sciences of the United States of America 110(51): 20651-20656.

Vorholter, F. J., et al. (2003). “Comparison of two Xanthomonas campestris pathovar campestris genomes revealed differences in their gene composition.” Journal of Biotechnology 106(2-3): 193-202.

Walsh, S. R., et al. (2010). “Full-length genome sequence analysis of enzootic nasal tumor virus reveals an unusually high degree of genetic stability.” Virus Research 151(1): 74-87.

Wang, D., et al. (2014). “Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits.” PLoS genetics 10(1).

Wang, D., et al. (2011). “Genome Sequencing Reveals Unique Mutations in Characteristic Metabolic Pathways and the Transfer of Virulence Genes between V. mimicus and V. cholerae.” PLoS ONE 6(6).

Wang, H. (2008). “Comparative analysis of teleost fish genomes reveals preservation of different ancient clock duplicates in different fishes.” Marine Genomics 1(2): 69-78.

Wang, W., et al. (2014). “The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.” Nature Communications 5.

Wang, Z.-N., et al. (2013). “Divergent evolutionary mechanisms of co-located Tak/Lrk and Glu-D3 loci revealed by comparative analysis of grass genomes.” Genome 56(4): 195-204.

Warren, W. C., et al. (2008). “Genome analysis of the platypus reveals unique signatures of evolution (vol 453, pg 175, 2008).” Nature 455(7210): 256-256.

Webb, K. M. and B. M. Rosenthal (2010). “Deep resequencing of Trichinella spiralis reveals previously un-described single nucleotide polymorphisms and intra-isolate variation within the mitochondrial genome.” Infection Genetics and Evolution 10(2): 304-310.

Wegmann, U., et al. (2014). “Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota (‘Ruminococcus bicirculans’) reveals two chromosomes and a selective capacity to utilize plant glucans.” Environmental Microbiology 16(9): 2879-2890.

Weigand, M. R., et al. (2014). “Genome Sequencing Reveals the Environmental Origin of Enterococci and Potential Biomarkers for Water Quality Monitoring.” Environmental Science & Technology 48(7): 3707-3714.

Wendland, J. and A. Walther (2011). “Genome Evolution in the Eremothecium Clade of the Saccharomyces Complex Revealed by Comparative Genomics.” G3-Genes Genomes Genetics 1(7): 539-548.

Wibberg, D., et al. (2011). “Complete genome sequencing of Agrobacterium sp H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.” Journal of Biotechnology 155(1): 50-62.

Wilkes, T. E., et al. (2010). “The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis.” Insect Molecular Biology 19: 59-73.

Wisniewski-Dye, F., et al. (2011). “Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments.” PLoS genetics 7(12).

Wittmann, J., et al. (2014). “First genome sequences of Achromobacter phages reveal new members of the N4 family.” Virology Journal 11.

Wong, S. S., et al. (2014). “Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing.” Nature Communications 5: 5477-5477.

Woo, P. C. Y., et al. (2006). “Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1.” Journal of Virology 80(14): 7136-7145.

Woo, P. C. Y., et al. (2007). “Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features.” Journal of Virology 81(4): 1574-1585.

Worden, A. Z., et al. (2009). “Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas.” Science 324(5924): 268-272.

Wu, C., et al. (2014). “The draft genome of the large yellow croaker reveals well-developed innate immunity.” Nature Communications 5: 5227-5227.

Wu, G. A., et al. (2014). “Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.” Nature Biotechnology 32(7): 656-+.

Wu, H., et al. (2014). “Camelid genomes reveal evolution and adaptation to desert environments.” Nature Communications 5.

Xia, Q., et al. (2009). “Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx).” Science 326(5951): 433-436.

Xu, A., et al. (2011). “The complete genome sequence of an enterovirus 76 isolate in China reveals a recombination event.” Archives of Virology 156(9): 1685-1689.

Xu, P., et al. (2011). “Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding.” Bmc Genomics 12.

Xu, X.-H., et al. (2014). “The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte.” Scientific Reports 4.

Xue, C., et al. (2014). “Draft Genome Sequence of Sphingobium sp. Strain BHC-A, Revealing Genes for the Degradation of Hexachlorocyclohexane.” Genome announcements 2(2).

Yagi, J. M., et al. (2009). “The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer.” Environmental Microbiology 11(9): 2253-2270.

Yang, L., et al. (2012). “Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly.” Plant Journal 71(6): 895-906.

Yin, H., et al. (2014). “Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.” Bmc Microbiology 14.

Yin, Y., et al. (2014). “A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily.” Bmc Genomics 15.

Yip, C. C. Y., et al. (2011). “Complete Genome Sequence of a Coxsackievirus A22 Strain in Hong Kong Reveals a Natural Intratypic Recombination Event.” Journal of Virology 85(22): 12098-12099.

Youssef, N. H., et al. (2013). “The Genome of the Anaerobic Fungus Orpinomyces sp Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader.” Applied and Environmental Microbiology 79(15): 4620-4634.

Yu, F., et al. (2014). “Comparison of complete genome sequences of dog rabies viruses isolated from China and Mexico reveals key amino acid changes that may be associated with virus replication and virulence.” Archives of Virology 159(7): 1593-1601.

Yu, M., et al. (2013). “Genome analysis of Pseudoalteromonas flavipulchra JG1 reveals various survival advantages in marine environment.” Bmc Genomics 14.

Zell, R., et al. (2012). “Sequencing of 21 Varicella-Zoster Virus Genomes Reveals Two Novel Genotypes and Evidence of Recombination.” Journal of Virology 86(3): 1608-1622.

Zhang, G., et al. (2012). “The oyster genome reveals stress adaptation and complexity of shell formation.” Nature 490(7418): 49-54.

Zhang, X. H. F. and L. A. Chasin (2006). “Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons.” Proceedings of the National Academy of Sciences of the United States of America 103(36): 13427-13432.

Zhao, W., et al. (2010). “Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism.” Cell Research 20(10): 1096-1108.

Zhao, Z., et al. (2014). “Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi (vol 14, pg 274, 2013).” Bmc Genomics 15.

Zhaxybayeva, O., et al. (2012). “Genome Sequence of the Mesophilic Thermotogales Bacterium Mesotoga prima MesG1.Ag.4.2 Reveals the Largest Thermotogales Genome To Date.” Genome Biology and Evolution 4(8): 812-820.

Zheng, Q., et al. (2012). “Gain and Loss of Phototrophic Genes Revealed by Comparison of Two Citromicrobium Bacterial Genomes.” PLoS ONE 7(4).

Zhou, A., et al. (2008). “Genome analysis reveals horizontal gene transfer in Penicillium marneffei.” International Journal of Infectious Diseases 12: S45-S45.

Zhou, C., et al. (2014). “The genome sequence of a novel simian adenovirus in a chimpanzee reveals a close relationship to human adenoviruses.” Archives of Virology 159(7): 1765-1770.

Zhou, X., et al. (2013). “Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.” Nature Communications 4.

Zhu, S., et al. (2012). “Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution.” Bmc Genomics 13.


Clearly, the purpose of genome sequencing is to “provide insights”.

Amemiya, C. T., et al. (2013). “The African coelacanth genome provides insights into tetrapod evolution.” Nature 496(7445): 311-316.

Anderson, I., et al. (2011). “Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes.” PloS one 6(5).

Angelov, A. and W. Liebl (2006). “Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea.” Journal of Biotechnology 126(1): 3-10.

Arnold, D. L., et al. (2009). Pseudomonas syringae Genomics Provides Important Insights to Secretion Systems, Effector Genes and the Evolution of Virulence.

Auernik, K. S., et al. (2008). “The genome sequence of the metal-mobilizing, extremely thermoacidophilic archaeon Metallosphaera sedula provides insights into bioleaching-associated metabolism.” Applied and Environmental Microbiology 74(3): 682-692.

Bachmann, N. L., et al. (2014). “Chlamydia genomics: providing novel insights into chlamydial biology.” Trends in Microbiology 22(8): 464-472.

Bakermans, C., et al. (2009). Genomic Insights into Cold Adaptation of Permafrost Bacteria. Soil Biology. R. Margesin. 16: 159-168.

Bannantine, J. P., et al. (2012). “Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association.” BMC Genomics 13.

Berthelot, C., et al. (2014). “The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.” Nature Communications 5.

Best, A. A., et al. (2004). “Evolution of eukaryotic transcription: Insights from the genome of Giardia lamblia.” Genome Research 14(8): 1537-1547.

Bhattacharyya, A., et al. (2002). “Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights.” Genome Research 12(10): 1556-1563.

Bogdanove, A. J., et al. (2011). “Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.” Journal of Bacteriology 193(19): 5450-5464.

Broadbent, J. R. and J. L. Steele (2007). Biochemistry of Cheese Flavor Development: Insights from Genomic Studies of Lactic Acid Bacteria. Flavor of Dairy Products. K. R. Cadwallader, M. Drake and R. J. McGorrin. 971: 177-192.

Brownlie, J. C. and S. L. O’Neill (2005). “Wolbachia genomes: Insights into an intracellular lifestyle.” Current Biology 15(13): R507-R509.

Bruggemann, H. (2005). “Insights in the pathogenic potential of Propionibacterium acnes from its complete genome.” Seminars in Cutaneous Medicine and Surgery 24(2): 67-72.

Bruggemann, H. and G. Gottschalk (2004). “Insights in metabolism and toxin production from the complete genome sequence of Clostridium tetani.” Anaerobe 10(2): 53-68.

Bruggemann, H., et al. (2005). “Hot genomics: Insights in the thermophilic lifestyle of Thermus thermophilus from its complete genome.” Journal of Biotechnology 118: S164-S164.

Bryant, D. A. and Z. Liu (2013). Green Bacteria: Insights into Green Bacterial Evolution through Genomic Analyses. Genome Evolution of Photosynthetic Bacteria. J. T. Beatty. 66: 99-150.

Buchrieser, C., et al. (2011). “Complete Genome Sequence of the Animal Pathogen Listeria ivanovii, Which Provides Insights into Host Specificities and Evolution of the Genus Listeria.” Journal of Bacteriology 193(23): 6787-6788.

Burmester, A., et al. (2011). “Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi.” Genome Biology 12(1).

Butler, J. E., et al. (2005). “The complete genome of Geobacter metalfireducens: Insights into degradation of aromatic compounds and electron transport via c-type cytochromes.” Abstracts of the General Meeting of the American Society for Microbiology 105: 559-560.

Cai, H., et al. (2009). “Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution.” Genome Biology and Evolution 1: 239-257.

Cai, Q., et al. (2014). “The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude (vol 14, R29, 2013).” Genome Biology 15(2).

Cardoso, J. C. R., et al. (2014). “Nematode and Arthropod Genomes Provide New Insights into the Evolution of Class 2 B1 GPCRs.” PloS one 9(3).

Cardoso, J. C. R., et al. (2014). “Fish genomes provide novel insights into the evolution of vertebrate secretin receptors and their ligand.” General and Comparative Endocrinology 209: 82-92.

Chaudhry, V., et al. (2013). “Insights from the draft genome of Paenibacillus lentimorbus NRRL B-30488, a promising plant growth promoting bacterium.” Journal of Biotechnology 168(4): 737-738.

Chen, S., et al. (2014). “Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.” Nature Genetics 46(3): 253-+.

Chen, Y. P., et al. (2013). “Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions.” BMC Genomics 14.

Cheng, S., et al. (2013). “The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers.” Plant Cell 25(8): 2813-2830.

Chong, T.-M., et al. (2012). “Insights from the Genome Sequence of Quorum-Quenching Staphylococcus sp Strain AL1, Isolated from Traditional Chinese Soy Sauce Brine Fermentation.” Journal of Bacteriology 194(23): 6611-6612.

Cock, J. M., et al. (2010). “The Ectocarpus genome sequence: insights into brown algal biology and the evolutionary diversity of the eukaryotes.” New Phytologist 188(1): 1-4.

Coda, A. B. and A. A. Sinha (2011). “Integration of genome-wide transcriptional and genetic profiles provides insights into disease development and clinical heterogeneity in Alopecia areata.” Genomics 98(6): 431-439.

Copley, S. D., et al. (2012). “The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway.” Genome Biology and Evolution 4(2): 184-198.

Corradi, N., et al. (2009). “Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions.” Genome Biology 10(10).

Coyne, R. S., et al. (2011). “Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.” Genome Biology 12(10).

Cubeta, M. A., et al. (2009). “Rhizoctonia solani genome project; providing insight into a link between beneficial and plant pathogenic fungi.” Phytopathology 99(6): S166-S166.

Dam, P., et al. (2011). “Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725.” Nucleic Acids Research 39(8): 3240-3254.

Davis, R. E., et al. (2004). “The Spiroplasma kunkelii genome: Insights to a parasitic lifestyle in insects and plants.” Phytopathology 94(6): S123-S123.

de Reuse, H. and S. Bereswill (2007). “Ten years after the first Helicobacter pylori genome: comparative and functional genomics provide new insights in the variability and adaptability of a persistent pathogen.” Fems Immunology and Medical Microbiology 50(2): 165-176.

Decatur, W. A., et al. (2013). “Insight from the lamprey genome: Glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropin-releasing hormone (GnRH).” General and Comparative Endocrinology 192: 237-245.

Dehal, P., et al. (2002). “The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins.” Science 298(5601): 2157-2167.

Denoeud, F., et al. (2014). “The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.” Science 345(6201): 1181-1184.

Depledge, D. P., et al. (2014). “Deep Sequencing of Viral Genomes Provides Insight into the Evolution and Pathogenesis of Varicella Zoster Virus and Its Vaccine in Humans.” Molecular Biology and Evolution 31(2): 397-409.

Deshpande, N. P., et al. (2013). “Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association.” BMC Genomics 14.

DiDonato, R. J., Jr., et al. (2005). “Complete genome sequence of Pelobacter carbinolicus: Insights into mechanisms of Fe(III) reduction and evolution of the family geobacteraceae.” Abstracts of the General Meeting of the American Society for Microbiology 105: 559-559.

Dishaw, L. J., et al. (2012). “The amphioxus genome provides unique insight into the evolution of immunity.” Briefings in Functional Genomics 11(2): 167-176.

Downing, T., et al. (2011). “Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.” Genome Research 21(12): 2143-2156.

Duan, C., et al. (2014). “Genomic and comparative genomic analyses of Rickettsia heilongjiangensis provide insight into its evolution and pathogenesis.” Infection Genetics and Evolution 26: 274-282.

Durfee, T., et al. (2008). “The complete genome sequence of Escherichia coli DH10B: Insights into the biology of a laboratory workhorse.” Journal of Bacteriology 190(7): 2597-2606.

Eikmeyer, F., et al. (2012). “The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.” Plasmid 68(1): 13-24.

Elkins, J. G., et al. (2008). “A korarchaeal genome reveals insights into the evolution of the Archaea.” Proceedings of the National Academy of Sciences of the United States of America 105(23): 8102-8107.

Engelthaler, D. M., et al. (2014). “Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal.” Mbio 5(4).

Eppinger, M., et al. (2009). “Complete Genome Sequence of Yersinia pestis Angola: New Insights into the Genome Evolution of the Plague Bacterium.” Abstracts of the General Meeting of the American Society for Microbiology 109.

Eppinger, M., et al. (2010). “Genome Sequence of the Deep-Rooted Yersinia pestis Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium.” Journal of Bacteriology 192(6): 1685-1699.

Espagne, E., et al. (2004). “Genome sequence of a polydnavirus: Insights into symbiotic virus evolution.” Science 306(5694): 286-289.

Fahey, B. and B. M. Degnan (2010). “Origin of animal epithelia: insights from the sponge genome.” Evolution & Development 12(6): 601-617.

Fan, Z., et al. (2014). “Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History.” Molecular Biology and Evolution 31(6): 1475-1489.

Fernandez-Fueyo, E., et al. (2012). “Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.” Proceedings of the National Academy of Sciences of the United States of America 109(14): 5458-5463.

Fischer, W., et al. (2009). “The complete genome sequence of Helicobacter pylori strain P12: Insights into gene transfer and genome evolution.” International Journal of Medical Microbiology 299: 24-24.

Fischer, W., et al. (2009). “The Complete Genome Sequence of H-pylori Strain P12: Insights into Gene Transfer and Genome Evolution.” Helicobacter 14(4): 334-334.

Foflonker, F., et al. (2013). “GENOME SEQUENCE OF BIOFUEL CANDIDATE ALGA PROVIDES INSIGHTS INTO STRESS ADAPTATION.” Phycologia 52(4): 31-31.

Foth, B. J., et al. (2014). “Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.” Nature Genetics 46(7): 693-700.

Fraser, C., et al. (2004). “Comparative genomics of the Bacillus anthracis family: insights into physiology and evolution of a pathogenic species.” Faseb Journal 18(8): C225-C226.

Fritz-Laylin, L. K., et al. (2011). “The Naegleria genome: a free-living microbial eukaryote lends unique insights into core eukaryotic cell biology.” Research in Microbiology 162(6): 607-618.

Furlong, R. F. (2005). “Insights into vertebrate evolution from the chicken genome sequence.” Genome Biology 6(2).

Gan, H. M., et al. (2013). “Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.” BMC Genomics 14.

Gibbs, R. A., et al. (2007). “Evolutionary and biomedical insights from the rhesus macaque genome.” Science 316(5822): 222-234.

Gibbs, R. A., et al. (2004). “Genome sequence of the Brown Norway rat yields insights into mammalian evolution.” Nature 428(6982): 493-521.

Gill, S. R., et al. (2005). “Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.” Journal of Bacteriology 187(7): 2426-2438.

Gillespie, J. J., et al. (2012). “A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle.” Journal of Bacteriology 194(2): 376-394.

Gioia, J., et al. (2006). “The genome sequence of Mannheimia haemolytica A1: Insights into virulence, natural competence, and Pasteurellaceae phylogeny.” Journal of Bacteriology 188(20): 7257-7266.

Gladieux, P., et al. (2014). “Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes.” Molecular Ecology 23(4): 753-773.

Gonzalez-Escalona, N., et al. (2013). “Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their Pathogenicity.” Genome announcements 1(5).

Gottschalk, G. and H. Brueggemann (2003). “Insights in metabolism and toxin production from the complete genome sequence of Clostridium tetani.” Anaerobe 9(4): 192-192.

Gramates, L. S. and C. Honeybee Genome Sequencing (2006). “Insights into social insects from the genome of the honeybee Apis mellifera (vol 443, pg 931, 2006).” Nature 444(7118): 512-512.

Graves, J. A. M. (2013). “Kangaroo gene mapping and sequencing: insights into mammalian genome evolution.” Australian Journal of Zoology 61(1): 4-12.

Green, N. M., et al. (2005). “Genome sequence of a serotype m28 strain of group A Streptococcus: Potential new insights into puerperal sepsis and bacterial disease specificity.” Journal of Infectious Diseases 192(5): 760-770.

Green, S., et al. (2010). “Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum.” PloS one 5(4).

Groenen, M. A. M., et al. (2012). “Analyses of pig genomes provide insight into porcine demography and evolution.” Nature 491(7424): 393-398.

Guimaraes, A. M. S., et al. (2011). “Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche.” PloS one 6(5).

Guinane, C. M., et al. (2011). “Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation.” Virulence 2(3): 241-243.

Gupta, B., et al. (2010). “Malaria parasite genome scan: insights into antimalarial resistance.” Parasitology Research 107(2): 495-499.

Hall, N. (2012). “Genomic insights into the other malaria.” Nature Genetics 44(9): 962-963.

Hatfull, G. F., et al. (2008). “Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution.” Research in Microbiology 159(5): 332-339.

Hayashida, K., et al. (2013). “Whole-Genome Sequencing of Theileria parva Strains Provides Insight into Parasite Migration and Diversification in the African Continent.” DNA Research 20(3): 209-220.

Hazell, S. L., et al. (1997). “Helicobacter pylori: metabolism, physiology and insights from the whole genome.” Baillieres Clinical Infectious Diseases 4(3): 283-317.

Heinz, E., et al. (2012). “The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution.” Plos Pathogens 8(10).

Herman, E. K., et al. (2011). “INITIAL INSIGHTS FROM THE NAEGLERIA FOWLERI GENOME INITIATIVE.” Journal of Phycology 47: S21-S22.

Hirt, R. P., et al. (2011). Trichomonas vaginalis Pathobiology: New Insights from the Genome Sequence. Advances in Parasitology, Vol 77. D. Rollinson and S. I. Hay. 77: 87-140.

Hori, C., et al. (2014). “Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood.” PLoS genetics 10(12): e1004759-e1004759.

Hu, T. T., et al. (2013). “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.” Genome Research 23(1): 89-98.

Huang, H., et al. (2012). “Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance.” Journal of Antimicrobial Chemotherapy 67(12): 2825-2832.

Huang, J., et al. (2014). “Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.” Scientific Reports 4.

Huang, Y., et al. (2013). “The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.” Nature Genetics 45(7): 776-+.

Imperi, F., et al. (2011). “The Genomics of Acinetobacter baumannii: Insights into Genome Plasticity, Antimicrobial Resistance and Pathogenicity.” Iubmb Life 63(12): 1068-1074.

Irisarri, I., et al. (2010). “The complete mitochondrial genome of the relict frog Leiopelma archeyi: Insights into the root of the frog Tree of Life.” Mitochondrial DNA 21(5): 173-182.

Ito, T., et al. (2003). “Insights on antibiotic resistance of Staphylococcus aureus from its whole genome: genomic island SCC.” Drug Resistance Updates 6(1): 41-52.

Jakubkova, M., et al. (2013). “Metabolism of hydroxyderivatives of benzene and benzoic acid in yeasts: an insight from analysis of complete yeast genomes.” Yeast 30: 164-164.

Jalan, N., et al. (2011). “Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificity.” Journal of Bacteriology 193(22): 6342-6357.

Jalan, N., et al. (2013). “Pan-genome analysis of Xanthomonas citri subsp citri provides insights into bacterial evolution and pathogenicity.” Phytopathology 103(6): 67-67.

Jalan, N., et al. (2013). “Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp citri provide insights into mechanisms of bacterial virulence and host range.” BMC Genomics 14.

Ji, B., et al. (2014). “Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp QH-2 strain.” Environmental Microbiology 16(2): 525-544.

Jiang, H., et al. (2013). “Comparative Genomic Analysis of Brucella melitensis Vaccine Strain M5 Provides Insights into Virulence Attenuation.” PloS one 8(8).

Jin, Q., et al. (2002). “Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.” Nucleic Acids Research 30(20): 4432-4441.

Joseph, S. J., et al. (2012). “Population Genomics of Chlamydia trachomatis: Insights on Drift, Selection, Recombination, and Population Structure.” Molecular Biology and Evolution 29(12): 3933-3946.

Kahlke, T., et al. (2012). “Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.” BMC Genomics 13.

Kalkum, M., et al. (2014). “Proteomics and Genomics Provide Novel Insights Into Streptomyces Lectin Biochemistry.” Glycobiology 24(11): 1115-1116.

Kang, Y. J., et al. (2014). “Genome sequence of mungbean and insights into evolution within Vigna species.” Nature Communications 5: 5443-5443.

Kasahara, M., et al. (2007). “The medaka draft genome and insights into vertebrate genome evolution.” Nature 447(7145): 714-719.

Khatri, I., et al. (2013). “Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii.” Gut Pathogens 5.

Kim, E. B., et al. (2011). “Genome sequencing reveals insights into physiology and longevity of the naked mole rat.” Nature 479(7372): 223-227.

Kim, S., et al. (2014). “Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.” Nature Genetics 46(3): 270-+.

Kimbrel, J. A., et al. (2011). “Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics.” Molecular Plant Pathology 12(6): 580-594.

Kirkness, E. F., et al. (2010). “Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.” Proceedings of the National Academy of Sciences of the United States of America 107(27): 12168-12173.

Klosterman, S. J., et al. (2011). “Verticillium comparative genomics yields insights into niche adaptation by plant vascular wilt pathogens.” Phytopathology 101(6): S208-S208.

Krause, J., et al. (2009). “Insights from sequencing the Neandertal genome.” American Journal of Physical Anthropology: 170-170.

Kroft, B. S., et al. (2013). “Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic Resistance.” Genome announcements 1(5).

Ku, C., et al. (2013). “Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma.” Genome Biology and Evolution 5(6): 1151-1164.

Kugita, M., et al. (2003). “The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants.” Nucleic Acids Research 31(2): 716-721.

Labigne, A. (2001). “The Helicobacter pylori genomes: new insights into physiopathology and therapeutic.” M S-Medecine Sciences 17(6-7): 712-719.

Lee, A. (1998). “The Helicobacter pylori genome – New insights into pathogenesis and therapeutics.” New England Journal of Medicine 338(12): 832-833.

Lee, K.-T., et al. (2013). “Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity.” BMC Genomics 14.

Leeb, T. (2007). “The Horse Genome Project – Sequence based insights into male reproductive mechanisms.” Reproduction in Domestic Animals 42: 45-50.

Lefevre, C. T., et al. (2013). “Comparative genomic analysis of magnetotactic bacteria from the Deltaproteobacteria provides new insights into magnetite and greigite magnetosome genes required for magnetotaxis.” Environmental Microbiology 15(10): 2712-2735.

Lemay, D. G., et al. (2009). “The bovine lactation genome: insights into the evolution of mammalian milk.” Genome Biology 10(4).

Lemieux, C., et al. (2014). “Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species.” BMC Genomics 15.

Li, C. et al. (2014). Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. GigaScience 3: 27.

Li, M., et al. (2014). “Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication.” Scientific Reports 4.

Li, X., et al. (2014). “The genome of Paenibacillus sabinae T27 provides insight into evolution, organization and functional elucidation of nif and nif-like genes.” BMC Genomics 15.

Lin, T., et al. (2014). “Genomic analyses provide insights into the history of tomato breeding.” Nature Genetics 46(11): 1220-1226.

Liu, D., et al. (2012). “The Genome of Ganderma lucidum Provide Insights into Triterpense Biosynthesis and Wood Degradation.” PloS one 7(5).

Liu, G.-H., et al. (2013). “The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny.” BMC Genomics 14: 1-13.

Liu, M.-J., et al. (2014). “The complex jujube genome provides insights into fruit tree biology.” Nature Communications 5.

Liu, Z., et al. (2010). “Evolution of Galanin Receptor Genes: Insights from the Deuterostome Genomes.” Journal of Biomolecular Structure & Dynamics 28(1): 97-106.

Lohr, J. E., et al. (2005). “Genomic analysis of bacteriophage Phi JL001: Insights into its interaction with a sponge-associated alpha-proteobacterium.” Applied and Environmental Microbiology 71(3): 1598-1609.

Lomma, M., et al. (2009). Legionella pneumophila – Host Interactions: Insights Gained from Comparative Genomics and Cell Biology. Microbial Pathogenomics. H. DeReuse and S. Bereswill. 6: 170-186.

Loper, J. E. (2005). “The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control.” Phytopathology 95(6): S144-S145.

Loper, J. E., et al. (2012). “Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions.” PLoS genetics 8(7).

Loper, J. E., et al. (2007). “The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control.” Phytopathology 97(2): 233-238.

Lv, Y., et al. (2012). “Genome Sequence of Corynebacterium glutamicum ATCC 14067, Which Provides Insight into Amino Acid Biosynthesis in Coryneform Bacteria.” Journal of Bacteriology 194(3): 742-743.

Ma, T., et al. (2013). “Genomic insights into salt adaptation in a desert poplar.” Nature Communications 4.

Maida, I., et al. (2014). “Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome.” Genomics 103(2-3): 229-238.

Martin, F., et al. (2008). “The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.” Nature 452(7183): 88-U87.

Maruyama, F., et al. (2009). “Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.” BMC Genomics 10.

Mattes, T. E., et al. (2008). “The genome of Polaromonas sp strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology.” Applied and Environmental Microbiology 74(20): 6405-6416.

McKenzie, S. K., et al. (2014). “Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins.” BMC Genomics 15.

McLeod, M. P., et al. (2006). “The complete genome of Rhodococcus sp RHA1 provides insights into a catabolic powerhouse.” Proceedings of the National Academy of Sciences of the United States of America 103(42): 15582-15587.

Meng, J., et al. (2013). “Genome and Transcriptome Analyses Provide Insight into the Euryhaline Adaptation Mechanism of Crassostrea gigas.” PloS one 8(3).

Mi, S., et al. (2011). “Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation.” Journal of Microbiology 49(6): 890-901.

Middleton, C. P., et al. (2014). “Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe.” PloS one 9(3).

Misner, I., et al. (2013). “Comparative genomic analyses of Rhizoctonia solani: Insights on evolution and pathogenesis.” Phytopathology 103(6): 98-98.

Mornico, D., et al. (2011). “Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia.” Genes 3(1): 35-61.

Moroz, L. L., et al. (2012). “The Genome of the Ctenophore Pleurobrachia bachei: Molecular Insights into Independent Origins of Nervous Systems.” Integrative and Comparative Biology 52: E125-E125.

Mullins, L. J. and J. J. Mullins (2004). “Insights from the rat genome sequence.” Genome Biology 5(5).

Nakagawa, I., et al. (2003). “Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution.” Genome Research 13(6): 1042-1055.

Nakagawa, S., et al. (2007). “Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens.” Proceedings of the National Academy of Sciences of the United States of America 104(29): 12146-12150.

Nascimento, A., et al. (2004). “Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis.” Journal of Bacteriology 186(7): 2164-2172.

Neha, J., et al. (2011). “Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity.” Journal of Bacteriology 193(22): 6342-6357.

Ogawa, Y., et al. (2011). “The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism’s Intracellular Adaptations.” Journal of Bacteriology 193(12): 2959-2971.

Okamura, Y., et al. (2005). “Comprehensive analysis of the ascidian genome reveals novel insights into the molecular evolution of ion channel genes.” Physiological Genomics 22(3): 269-282.

Okubo, T., et al. (2012). “Complete Genome Sequence of Bradyrhizobium sp S23321: Insights into Symbiosis Evolution in Soil Oligotrophs.” Microbes and Environments 27(3): 306-315.

Olson, M. V. and A. Varki (2003). “Sequencing the chimpanzee genome: Insights into human evolution and disease.” Nature Reviews Genetics 4(1): 20-28.

Page, J. T., et al. (2013). “Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing.” G3-Genes Genomes Genetics 3(10): 1809-1818.

Paixao-Cortes, V. R., et al. (2012). “Homo sapiens, Homo neanderthalensis and the Denisova specimen: New insights on their evolutionary histories using whole-genome comparisons.” Genetics and Molecular Biology 35(4): 904-U210.

Palenik, B., et al. (2007). “The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.” Proceedings of the National Academy of Sciences of the United States of America 104(18): 7705-7710.

Palenik, B., et al. (2006). “Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.” Proceedings of the National Academy of Sciences of the United States of America 103(36): 13555-13559.

Palmer, G. H., et al. (2006). Insights into mechanisms of bacterial antigenic variation derived from the complete genome sequence of Anaplasma marginale. Century of Rickettsiology: Emerging, Reemerging Rickettsioses, Molecular Diagnostics, and Emerging Veterinary Rickettsioses. K. E. Hechemy, J. A. Oteo, D. A. Raoult, D. J. Silverman and J. R. Blanco. 1078: 15-25.

Parizzi, L. P., et al. (2012). “The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential.” BMC Genomics 13.

Peng, X., et al. (2007). “Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms.” Virology 364(1): 237-243.

Pfister, L. A., et al. (2008). “Full genome comparisons of Mycobacterium: Insight into the origin of tuberculosis and leprosy.” American Journal of Physical Anthropology: 171-171.

Picardeau, M., et al. (2008). “Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis.” PloS one 3(2).

Pieretti, I., et al. (2009). “The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae.” BMC Genomics 10.

Polashock, J., et al. (2014). “The American cranberry: first insights into the whole genome of a species adapted to bog habitat.” Bmc Plant Biology 14.

Procopio, L., et al. (2012). “Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential.” Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 101(2): 289-302.

Purushe, J., et al. (2010). “Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche.” Microbial Ecology 60(4): 721-729.

Qi, J., et al. (2013). “A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity.” Nature Genetics 45(12): 1510-U1149.

Qin, C., et al. (2014). “Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization.” Proceedings of the National Academy of Sciences of the United States of America 111(14): 5135-5140.

Qin, L., et al. (2013). “Genomic analysis of vaccinia virus strain TianTan provides new insights into the evolution and evolutionary relationships between Orthopoxviruses.” Virology 442(1): 59-66.

Que, Y., et al. (2014). “Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut.” BMC Genomics 15: 996-996.

Ralser, M., et al. (2012). “The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt.” Open Biology 2.

Rands, C. M., et al. (2013). “Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence.” BMC Genomics 14: 1-15.

Reguera, G., et al. (2004). “Genome-wide analysis of Geobacter sulfurreducens biofilms: Novel insights into the regulation of community development and electron transfer.” Abstracts of the General Meeting of the American Society for Microbiology 104: 541-541.

Renfree, M. B., et al. (2011). “Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development (vol 12, pg R81, 2011).” Genome Biology 12(12).

Rensing, S. A., et al. (2008). “The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.” Science 319(5859): 64-69.

Ricaldi, J. N., et al. (2012). “Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity.” Plos Neglected Tropical Diseases 6(10).

Roney, G., et al. (2009). “The Genome Sequence of a Human Isolate of Lancefield Group C Streptococcus Yields Novel Insights into Virulence Evolution in Pyogenic Streptococci.” Abstracts of the General Meeting of the American Society for Microbiology 109.

Rotman, E., et al. (2012). “Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment.” Journal of Bacteriology 194(24): 6802-6817.

Rudenko, G. (2012). “High-throughput whole genome analysis provides insight into how the major drugs against African sleeping sickness operate.” Pathogens and Global Health 106(2): 79-79.

Rusniok, C., et al. (2010). “Genome Sequence of Streptococcus gallolyticus: Insights into Its Adaptation to the Bovine Rumen and Its Ability To Cause Endocarditis.” Journal of Bacteriology 192(8): 2266-2276.

Ryan, J. F., et al. (2013). “The Genome of the Ctenophore, Mnemiopsis leidyi: Insights into the Genetics of Innovation and the Evolution of Multicellularity.” Integrative and Comparative Biology 53: E187-E187.

Samollow, P. B. (2008). “The opossum genome: Insights and opportunities from an alternative mammal.” Genome Research 18(8): 1199-1215.

Sanggaard, K. W., et al. (2014). “Spider genomes provide insight into composition and evolution of venom and silk (vol 5, 3765, 2014).” Nature Communications 5.

Santos-Garcia, D., et al. (2014). “The Genome of Cardinium cBtQ1 Provides Insights into Genome Reduction, Symbiont Motility, and Its Settlement in Bemisia tabaci.” Genome Biology and Evolution 6(4): 1013-1030.

Sato, S., et al. (2012). “The tomato genome sequence provides insights into fleshy fruit evolution.” Nature 485(7400): 635-641.

Savijoki, K., et al. (2014). “Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains.” Journal of Proteome Research 13(8): 3748-3762.

Schartl, M., et al. (2013). “The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits.” Nature Genetics 45(5): 567-U150.

Schoen, C., et al. (2008). “Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.” Proceedings of the National Academy of Sciences of the United States of America 105(9): 3473-3478.

Schoen, C., et al. (2007). “Living in a changing environment: Insights into host adaptation in Neisseria meningitidis from comparative genomics.” International Journal of Medical Microbiology 297(7-8): 601-613.

Schroeder, J., et al. (2011). “Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation.” BMC Genomics 12.

Seim, I., et al. (2013). “Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii.” Nature Communications 4.

Setubal, J. C., et al. (2009). The Genomics of Agrobacterium: Insights into its Pathogenicity, Biocontrol and Evolution.

Shaffer, B. (2013). “Painted Turtle Genome Offers Insights into Chelonian Phylogeny, Evolution, and Physiology.” Herpetological Review 44(2): 182-183.

Shahinas, D., et al. (2013). “Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics.” PloS one 8(6).

Shittu, A. O., et al. (2007). “Insights on virulence and antibiotic resistance: A review of the accessory genome of Staphylococcus aureus.” Wounds-a Compendium of Clinical Research and Practice 19(9): 237-244.

Sieber, J. R., et al. (2010). “The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production.” Environmental Microbiology 12(8): 2289-2301.

Sjodin, A., et al. (2012). “Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish.” BMC Genomics 13.

Sloan, D. B. (2013). “One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure.” New Phytologist 200(4): 978-985.

Smith, J. J., et al. (2013). “Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.” Nature Genetics 45(4): 415-421.

Soanes, D. M., et al. (2007). “Insights from sequencing fungal and oomycete genomes: What can we learn about plant disease and the evolution of pathogenicity?” Plant Cell 19(11): 3318-3326.

Sower, S. A., et al. (2009). Insight from Lamprey Genomics: Brain and Pituitary Reproductive Hormones of Lampreys. Biology, Management, and Conservation of Lampreys in North America. L. R. Brown, S. D. Chase, M. G. Mesa, R. J. Beamish and P. B. Moyle. 72: 57-70.

Spang, A., et al. (2012). “The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations.” Environmental Microbiology 14(12): 3122-3145.

Sridhar, S., et al. (2012). “Whole genome sequencing of the fish pathogen Francisella noatunensis subsp orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity.” BMC Genomics 13.

Stabler, R. A., et al. (2009). “Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.” Genome Biology 10(9).

Steele, R. E. (2012). “The Hydra genome: insights, puzzles and opportunities for Developmental Biologists.” International Journal of Developmental Biology 56(6-8): 535-542.

Stinear, T. P., et al. (2008). “Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.” Genome Research 18(5): 729-741.

Studholme, D. J., et al. (2011). “Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.” Genes 2(4): 1050-1065.

Stukenbrock, E. H., et al. (2011). “The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species.” Genome Research 21(12): 2157-2166.

Suen, G., et al. (2011). “The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle.” PLoS genetics 7(2).

Supply, P., et al. (2013). “Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis.” Nature Genetics 45(2): 172-179.

Swine Genome Sequencing, C. (2012). “Analyses of pig genomes provide insight into porcine demography and evolution.” Nature, UK 491(7424): 393-398.

Swore, J. J., et al. (2013). “On the Origins of Glutamatergic Signaling: Insights from the ctenophore genome (Pleurobrachia bachei).” Integrative and Comparative Biology 53: E211-E211.

Tachibana, S.-I., et al. (2012). “Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.” Nature Genetics 44(9): 1051-+.

Thomson, N. R., et al. (2008). “Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.” Genome Research 18(10): 1624-1637.

Tisserant, E., et al. (2014). “Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (vol 110, pg 20117, 2013).” Proceedings of the National Academy of Sciences of the United States of America 111(1): 563-563.

Tisserant, E., et al. (2013). “Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.” Proceedings of the National Academy of Sciences of the United States of America 110(50): 20117-20122.

Tomato Genome, C. (2012). “The tomato genome sequence provides insights into fleshy fruit evolution.” Nature, UK 485(7400): 635-641.

Toome, M., et al. (2014). “Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae.” New Phytologist 202(2): 554-564.

Travisany, D., et al. (2014). “A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.” Research in Microbiology 165(9): 743-752.

Triplett, L. R. (2012). “Draft genomic sequence of rice pathogens and nonpathogens: Insights in biology, diversity, and diagnosis.” Phytopathology 102(7): 158-158.

Trost, E., et al. (2010). “The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.” BMC Genomics 11.

Trotter, M., et al. (2006). “Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactic provides insight into its adaptable nature.” Gene 366(1): 189-199.

Valdes, J., et al. (2011). “Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus.” Journal of Bacteriology 193(24): 7003-7004.

Veneault-Fourrey, C., et al. (2014). “Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment.” Fungal Genetics and Biology 72: 168-181.

Venkatesh, B., et al. (2014). “Elephant shark genome provides unique insights into gnathostome evolution.” Nature 505(7482): 174-179.

Voelker, M., et al. (2009). “How conserved are bird genomes? Insights from the chicken and zebra finch genome projects.” Chromosome Research 17(4): 577-577.

Wallberg, A., et al. (2014). “A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.” Nature Genetics 46(10): 1081-1088.

Wang, L., et al. (2014). “Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis.” Genome Biology 15(2).

Wang, Q., et al. (2009). “Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches.” PloS one 4(10).

Wang, S., et al. (2014). “Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics.” BMC Genomics 15.

Wang, W., et al. (2014). “The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.” Nature Communications 5.

Wang, X., et al. (2014). “The locust genome provides insight into swarm formation and long-distance flight.” Nature Communications 5: 1-9.

Wang, Y., et al. (2011). “The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses.” Virus Genes 42(3): 444-456.

Wang, Y., et al. (2013). “The sacred lotus genome provides insights into the evolution of flowering plants.” Plant Journal 76(4): 557-567.

Wang, Z., et al. (2013). “The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.” Nature Genetics 45(6): 701-+.

Ward, N., et al. (2004). “Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath).” Plos Biology 2(10): 1616-1628.

Ward, N. L., et al. (2009). “Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils.” Applied and Environmental Microbiology 75(7): 2046-2056.

Watanabe, T., et al. (2012). “Draft Genome Sequence of a Psychrotolerant Sulfur-Oxidizing Bacterium, Sulfuricella denitrificans skB26, and Proteomic Insights into Cold Adaptation.” Applied and Environmental Microbiology 78(18): 6545-6549.

Watanabe, T., et al. (2014). “Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: Genetic insights into the sulfur oxidation pathway of betaproteobacteria.” Systematic and Applied Microbiology 37(6): 387-395.

Waters, E., et al. (2003). “The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism.” Proceedings of the National Academy of Sciences of the United States of America 100(22): 12984-12988.

Wisniewski-Dye, F., et al. (2012). “Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation.” Genes 3(4): 576-602.

Worley, K. C., et al. (2014). “The common marmoset genome provides insight into primate biology and evolution.” Nature Genetics 46(8): 850-857.

Wu, D. and B. G. Turgeon (2013). “Setosphaeria rostrata: Insights from the sequenced genome of Setosphaeria turcica.” Fungal Genetics and Biology 61: 158-163.

Xie, B.-B., et al. (2014). “Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style.” Genome Biology and Evolution 6(2): 379-390.

Yap, H.-Y. Y., et al. (2014). “The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties.” BMC Genomics 15.

Yap, K.-P., et al. (2012). “Insights from the Genome Sequence of a Salmonella enterica Serovar Typhi Strain Associated with a Sporadic Case of Typhoid Fever in Malaysia.” Journal of Bacteriology 194(18): 5124-5125.

Ye, C.-Y., et al. (2014). “Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species.” PloS one 9(11): e113657-e113657.

Yin, H., et al. (2014). “Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.” Bmc Microbiology 14.

Yin, Y., et al. (2014). “A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily.” BMC Genomics 15.

Yoshida-Takashima, Y., et al. (2013). “Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages.” Extremophiles 17(3): 405-419.

You, M., et al. (2013). “A heterozygous moth genome provides insights into herbivory and detoxification.” Nature Genetics 45(2): 220-225.

You, X., et al. (2014). “Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.” Nature Communications 5: 5594-5594.

Young, N. D., et al. (2011). “The Medicago genome provides insight into the evolution of rhizobial symbioses.” Nature 480(7378): 520-524.

Young, N. D., et al. (2014). “The Opisthorchis viverrini genome provides insights into life in the bile duct.” Nature Communications 5.

Yu, J.-K., et al. (2008). “Insights from the amphioxus genome on the origin of vertebrate neural crest.” Genome Research 18(7): 1127-1132.

Yuan, M., et al. (2012). “Genome Sequence and Transcriptome Analysis of the Radioresistant Bacterium Deinococcus gobiensis. Insights into the Extreme Environmental Adaptations.” PloS one 7(3).

Yun, W., et al. (2013). “The sacred lotus genome provides insights into the evolution of flowering plants.” Plant Journal 76(4): 557-567.

Zeigler, D. R. (2011). “The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics.” Microbiology-Sgm 157: 2033-2041.

Zhan, S., et al. (2011). “The Monarch Butterfly Genome Yields Insights into Long-Distance Migration.” Cell 147(5): 1171-1185.

Zhan, X., et al. (2013). “Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle.” Nature Genetics 45(5): 563-U142.

Zhang, G., et al. (2013). “Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity.” Science 339(6118): 456-460.

Zhang, G., et al. (2012). “Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.” Nature Biotechnology 30(6): 549.

Zhang, G., et al. (2014). Comparative Genomics Reveal Insights into Avian Genome Evolution and Adaptation. Science 346: 1311-1320.

Zhang, T., et al. (2012). “The Complete Chloroplast and Mitochondrial Genome Sequences of Boea hygrometrica: Insights into the Evolution of Plant Organellar Genomes.” PloS one 7(1).

Zhao, S., et al. (2013). “Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation.” Nature Genetics 45(1): 67-U99.

Zhou, D., et al. (2014). “Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites.” BMC Genomics 15.

Zhou, X., et al. (2013). “Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.” Nature Communications 4.

Zhou, X., et al. (2014). “Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.” Nature Genetics 46(12): 1303-1310.

Zhu, L., et al. (2013). “Complete Genome Analysis of Three Acinetobacter baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements.” PloS one 8(6).

Zimmer, A. D., et al. (2013). “Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions.” BMC Genomics 14.


Were introns immediately dismissed as useless junk?

In a recent paper, Morris and Mattick (2014) claim that:

“The discovery of introns in 1977  was perhaps the biggest surprise in the history of molecular biology, as no one expected that the genes of higher organisms would be mosaics of coding and non-coding sequences, all of which are transcribed. However, the prevailing concept of the flow of genetic information was not overly disturbed, as the removal of the intervening sequences (that is, introns) and the reconstruction of a mature mRNA by splicing preserved the conceptual status quo; that is, genes still made proteins. In parallel, it was assumed that the excised intronic RNAs were simply degraded, although the technology of the time was too primitive to confirm this. In any case, introns were immediately and universally dismissed as genomic debris, and their presence was rationalized as evolutionary remnants involved in the prebiotic modular assembly of protein-coding RNAs that have remained (and been expanded by transposition) in complex organisms. This notion was consistent, at least superficially, with the implication of the C-value enigma that eukaryotes contained varying amounts of DNA ‘baggage’. It is also in agreement with the accompanying conclusion that retrotransposon sequences are mainly ‘selfish’, parasitic DNA.”

Morris, K.V. and J.S. Mattick (2014). The rise of regulatory RNA. Nature Reviews Genetics, in press.

So, let’s check the actual literature of the time and see if their version is correct:

“Perhaps the most surprising discovery in the initial studies of eukaryotic gene structure has been that many genes contain interruptions in the coding sequences. The origin and the function of these intervening sequences (IVS or introns) are not yet well understood but are the subject of intense investigation.”

Wallace, R.B., P.F. Johnson, S. Tanaka, M. Schöld, K. Itakura, and J. Abelson. 1980. Directed deletion of a yeast transfer RNA intervening sequence. Science 209: 1396-1400.

“Since the discovery that many eukaryotic genes are discontinuous, a number of studies have been directed towards identifying a function for intervening sequences (IVSs).”

Johnson, P.F. and J. Abelson. 1983. The yeast tRNA(tyr) gene intron is essential for correct modification of its tRNA product. Nature 302: 681-687.

“It is possible that the relationship between the location of the splice junction in the gene at the surface of the protein confers a biological advantage and hence is a result of natural selection. Introns and their associated splicing systems could be exploited in many ways during the evolution of a protein.”

Craik, C.S., S. Sprang, R. Fletterick, and W.J. Rutter. 1982. Intron-exon splice junctions map at protein surfaces. Nature 299: 180-182.

“We conclude from this experiment that the intron in the yeast actin gene does not have an observable function. It is possible that the role of the intron is too subtle to be observed in laboratory conditions of growth or that the intron, while having evolutionary significance, has no present role. To conclude that this is true for all yeast genes that contain introns would of course be premature, but there exist strains in which mitochondrial introns have been removed with no observable effect.”

Ng, R., H. Domdey, G. Larson, J.J. Rossi, and J. Abelson. 1985. A test for intron function in the yeast actin gene. Nature 314: 183-184.

“Solutions to problems of how introns are dealt with by cells do not address the question of why introns are there at all, questions about intron function. Some introns in some genes perform clearly regulatory roles, since splicing factors specific to the tissue or developmental stage decide when and where splicing should occur (Breitbart et al. 1985). In addition, some introns in some genes contain enhancers or modulators of the expression of those genes (Slater et al. 1985). However, the great majority of introns in protein-coding genes have no such “functions.” Direct experimental as well as indirect comparative data show that most introns can be removed from genes without phenotypic effect (Blake 1985). Thus, in terms of beneficial effects on the fitnesses of organisms, we almost certainly cannot account for the presence of the majority of individual introns, nor for the propensity to have introns at all, even though introns may on the average represent as much as 90% of the length of a gene and perhaps as much as half of the total DNA in some complex eukaryotes such as humans.”

Doolittle, W.F. 1987. The origin and function of intervening sequences in DNA: a review. American Naturalist 130: 915-928.

“Ever since the discovery of split genes, there has been a debate about why they are split. This can be resolved into three separate problems: the origin of the introns that split the genes (separating exons from each other), the role of introns in evolution, and their present function, if any.”

Rogers, J. 1985. Exon shuffling and intron insertion in serine protease genes. Nature 315: 458-459.

“These conserved sequences, especially those found in the introns, suggest a role for internal sequences in the regulation of β-actin gene expression.”

Ng, S.-Y., P. Gunning, R. Eddy, P. Ponte, J. Leavitt, T. Shows, and L. Kedes. 1985. Evolution of the functional human β-actin gene and its multi-pseudogene family: conservation of noncoding regions and chromosomal dispersion of pseudogenes. Molecular and Cellular Biology 5: 2720-2732.

“The advantage to the organism to remove intron 1 last is unclear but could point to some as yet undetermined function for this intron. In support of this, we have found that a DNA probe derived from intron 1 hybridizes to a single fragment in a Southern blot of total mouse genomic DNA indicating that the sequences in this intron may be conserved, whereas a DNA probe derived from intron 2 does not hybridize.”

Wells, D., D. Hoffman, and L. Kedes. 1987. Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family. Nucleic Acids Research 15: 2871-2889.

1993 Nobel Prize in Physiology or Medicine
to Richard J. Roberts and Phillip A. Sharp
For their discovery of split genes

“Roberts’ and Sharp’s discovery has changed our view on how genes in higher organisms develop during evolution. The discovery also led to the prediction of a new genetic process, namely that of splicing, which is essential for expressing the genetic information. The discovery of split genes has been of fundamental importance for today’s basic research in biology, as well as for more medically oriented research concerning the development of cancer and other diseases.”

“As a consequence of the discovery that genes are often split, it seems likely that higher organisms in addition to undergoing mutations may utilize another mechanism to speed up evolution: rearrangement (or shuffling) of gene segments to new functional units. This can take place in the germ cells through crossing-over during pairing of chromosomes. This hypothesis seems even more attractive following the discovery that individual exons in several cases correspond to building modules in proteins, so-called domains, to which specific functions can be attributed. An exon in the genome would thus correspond to a particular subfunction in the protein and the rearrangement of exons could result in a new combination of subfunctions in a protein. This kind of process could drive evolution considerably by rearranging modules with specific functions.”

http://nobelprize.org/nobel_prizes/medicine/laureates/1993/press.html


Susumu Ohno did not coin the term “junk DNA” — a must-read by Dan Graur.

 

Anyone interested in the topic of “junk DNA” should go and read this fine piece of detective work by Dan Graur immediately!

http://judgestarling.tumblr.com/post/64504735261/the-origin-of-junk-dna-a-historical-whodunnit

 


Some big news about Evolution: Education and Outreach.

lAs many of my academic friends know, I started out as a member of the Editorial Board when the journal was launched, and then became an Associate Editor as well as a guest Editor for a special issue on eye evolution. When the journal ceased to be open-access, I resigned from the Editorial Board in protest, but have since returned now that free access has been restored. Since then, I have been Senior Handling Editor (which is more or less the same as Associate Editor in practice).

Well, after some discussion with Niles Eldredge, who has been Co-Editor-in-Chief along with his son Greg since the journal’s inception, it looks like my position with the journal is changing again.

You see, Niles feels that he’s ready to cut back on his involvement now that he is of retirement age (and, I must say, well deserving of a rest!).

And so, effective fairly soon, I will be the new Co-Editor-in-Chief of the journal, with a special emphasis on the science content (Greg will continue with his focus on educational topics).

Fellow biologist friends: be forewarned that I will be pestering you soon to contribute a manuscript to the journal…


Genome reduction in bladderworts vs. leg loss in snakes.

In one sense, I am happy that there is enough interest in the concept of “junk DNA” (and by extension, my area of research in genome size evolution) that the subject gets regular media attention. A few months ago, it was all about the ENCODE project and its “finding” of “function” for 80% of the human genome. This week, it’s a story that has the exact opposite message: that large amounts of so-called “junk DNA” can be deleted without apparent consequence. This most recent story was prompted by the publication of the genome sequence of the carnivorous plant known as the floating bladderwort. This plant is of interest because it has a very small genome that is nearly devoid of transposable elements and other non-coding DNA, while also containing more protein-coding genes than the human genome and exhibiting signs of past genome duplication events. We’ve known that the genome was small for several years, but having the genome sequence provides some important insights into what a genome this size contains, and (most interestingly) what it doesn’t.

In typical style, Ed Yong has written up a very nice summary of the paper and the potential implications for the junk DNA debate. Following the lead of the original paper and the associated press release, many media reports similarly took the “this plant can get rid of junk DNA, so maybe it isn’t functional after all” line (a few examples: here, here, and here).

I was quoted in Ed Yong’s article as follows:

“The study further challenges simplistic accounts of genome biology that assume functions for most or all DNA sequences, without addressing the enormous variability in genome size among plants and animals,” says T. Ryan Gregory, who studies the evolution of genome sizes at the University of Guelph.

In 2007, Gregory coined the “Onion Test” to challenge anyone who thinks that non-coding DNA isn’t junk. If that DNA is important, why is it that the onion needs so much more of it than a human, or even other closely related plants? “The Onion Test could just as easily have been called the Bladderwort Test,” he says. “If non-coding DNA is vital for gene regulation or some similar function, then how can a plant such as the bladderwort get by with so little of it?”

For me, the logic of the authors of the paper is straightforward. Here we have a complex plant with a lot of genes but very little non-coding DNA, and this calls into question the idea that you need a lot of non-coding DNA to regulate genes in a complex organism. Jonathan Eisen, on the other hand, has objected in his usual snarky way, awarding MSNBC and the authors of the bladderwort genome paper one of his “Twisted Tree of Life Awards”. As he summarizes the claim,

So – basically – if ONE FUCKING ORGANISM DELETES SOME OF IT’S [sic] NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

In the comments thread on his blog post, he expanded on what he sees as the problem with this argument:

The fact that a plant can function without much non coding DNA really says nothing about the function or role of such non coding DNA in other species. All it says it that such non coding DNA is not absolutely essential for a plant to function. But this plant lineage could have evolved new means of regulation or other functions that were found in the non coding DNA of its ancestors. Or, in other words, a plant with a small genome says as much about non coding DNA in other plants and in humans as a fish with no eyes says about the role of eyes in vertebrates that see. Or should I try another? This says as much about the role of non coding DNA in other plants as the existence of snakes say about the role of legs. And so on.

And – there is no doubt that eyeless fish and limbless reptiles tell us an enormous amount. They tell us, for example, that eyes are non absolutely necessary for fish to function. And their adaptations to being eyeless tell us all sorts of great things about senses. But the existence of eyeless fish does not tell us that eyes are useless in fish.

Here is how I see the logic:

Most plants have junk DNA
One lineage doesn’t and the plants seem pretty OK.
Therefore junk DNA is useless

Most reptiles have legs
One lineage doesn’t have legs and these seem pretty OK.
Therefore legs are useless.

Isn’t that the logic here?

No, that isn’t the logic, and the legless snakes or eyeless cave fishes analogy is flawed. Why?

1. We know that legs and eyes are functional, and we know what they are functional for (walking and seeing, respectively). By contrast, we do not have strong evidence that non-coding DNA is functional or what it may be functional for. Worse, the very existence of so much non-coding DNA itself is taken as “evidence” that it must be doing something. Therefore, the observation of a plant that lacks a substantial amount of non-coding DNA but gets by just fine suggests that this kind of DNA isn’t strictly necessary in order to make a complex plant.

2. If most of the non-coding DNA in a larger genome does serve an important regulatory function, then it means this plant with a tiny genome must have evolved a totally different system for regulating its genes. This strikes me as a rather large assumption — and in any case, it’s one for which we have no evidence. As such, I would argue that it is at least as parsimonious to take this small genome as evidence that non-coding DNA in general does not serve a key regulatory function for the most part.

3. When snakes lost their legs or cave fishes lost their eyes, they also lost the specific ability that legs or eyes provided. Legless snakes can’t walk, because the function of legs is walking. Eyeless fishes can’t see, because the function of eyes is seeing. The proposed function for non-coding DNA is gene regulation. Unlike the snake or fish example, the bladderwort has lost most of its non-coding DNA but it can still regulate all of its genes just fine.

I think Jonathan raises a valid point about the dangers of overzealous extrapolation, but I think his criticism of the authors (much less its tone) in this case is unwarranted.


Moore’s Law, the origin of life, and dropping turkeys off a building.

I’ve already mentioned the nonsensical paper “published” in (surprise, surprise) arXiv in which the authors claim that the origin of life occurred long before the origin of the Earth based on the application of Moore’s Law to DNA. I won’t go into all the reasons that this is silly — for that, you can see critiques by PZ Myers and Massimo Pigliucci. Suffice it to say that the data, the analysis, and the interpretation are all problematic.

Notably, the authors present this figure, which more or less sums up what is wrong with the entire paper.

07-05-2013 3-10-28 PM

As I saw this, I couldn’t help but feel like it reminded me of some other extrapolation I had seen years ago. And today it came to me — cooking a turkey by dropping it off a roof! Or rather, by converting potential energy into kinetic energy. Here’s the figure from the very funny article, which was published in the Journal of Irreproducible Results.

07-05-2013 3-09-04 PM

07-05-2013 3-26-18 PM


ENCODE quote compilation.

Here’s a short compilation I made for use in a recent presentation on ENCODE and the claim that 80% of the human genome is functional. These are quotes from ENCODE project leaders and the senior editor of Nature. It is not surprising that the story presented by the media was that ENCODE had destroyed the concept of “junk DNA”, given that this is what the researchers themselves said.

Sources:

http://www.youtube.com/watch?v=yjpW30z-SB8

http://www.youtube.com/watch?v=PsV_sEDSE2o

http://www.youtube.com/watch?v=Y3V2thsJ1Wc

http://www.youtube.com/watch?v=KiwXtHRfBC8


Critiques of ENCODE in peer-reviewed journals.

There has been lots of talk (including some in the media; see here and here and here) about the Graur et al. (2013) paper in GBE which was critical of ENCODE, much of it focusing on the tone of the paper. While the Graur et al. (2013) paper certainly doesn’t pull any punches in terms of ENCODE’s outrageous claims and incredible media hype, it also contains a number of important criticisms of the science underlying the project. Graur et al. (2013) were not the only ones to publish peer-reviewed critiques, and I expect that the list will continue to expand.

Here is a list of the papers that have appeared to date:

Doolittle, W.F. (2013). Is junk DNA bunk? A critique of ENCODE. Proceedings of the National Academy of Sciences USA 110: 5294–5300.

Eddy, S.R. (2012). The C-value paradox, junk DNA and ENCODE. Current Biology 22: R898–R899.

Eddy, S.R. (2013). The ENCODE project: Missteps overshadowing a success. Current Biology 23: R259–R261.

Graur, D., Y. Zheng, N. Price, R.B.R. Azevedo, R.A. Zufall, and E. Elhaik. (2013). On the immortality of television sets: “Function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution 5: 578-590.

Niu, D.-K. and L. Jiang. (2013). Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and Biophysical Research Communications 430: 1340-1343.

Hurst, L.D. (2013). Open questions: A logic (or lack thereof) of genome organization. BMC Biology 11: 58.

Some of these authors have written blogs, in some cases to go after each other (stay tuned — there may be more debate coming).

Sean Eddy: ENCODE says what?

Dan Graur: Sean Eddy knows on which side the bread is buttered: Better be on the side of “good-science funding” than on the side of “good science”.

Dan Graur: Laurence Hurst’s error: the inability to distinguish between a stupid animal, a dead animal, and the elephant in the room