Genomes large and small.

The past few years have witnessed the discovery of both very large and small genomes in different groups of organisms. Here are some highlights from this research.

The first represents the largest genome so far reported for a crustacean, in the Arctic-dwelling amphipod Ampelisca macrocephala. The genome of this small invertebrate is a whopping 63.2 billion base pairs, or about 20 times larger than the human genome (Rees et al. 2007). Again, this sort of observation should dispel the notion that all non-coding DNA is functional for protecting against mutagens or some such thing.

The second interesting finding is of the largest viral genome so far discovered. The virus, dubbed Mimivirus, was sufficiently odd that it was originally assumed to be a bacterium when first observed, but on closer examination was found to be a virus. Its genome size is estimated as 1.2 million bases, which is larger than the genome of many bacteria (Raoult et al 2007). So, now there is overlap in reported genome sizes between viruses and bacteria, which goes along with the known overlap between the genome sizes of bacteria and eukaryotes (Gregory 2005).

And now for some small genomes. More specifically, the smallest flowering plant genome, that of Genlisea margaretae at a mere 63 million base pairs, less than half the size of the previous record holder, Arabidopsis thaliana at about 157 million base pairs. This increases the range in angiosperm genome sizes to more than 2,000-fold. (In animals the total range is about 3,300-fold; Gregory et al. 2007).

The smallest insect genome so far estimated was reported fairly recently as well. It belongs to Caenocholax fenyesi, a twisted-wing parasite, and is a mere 108 million base pairs (Johnston et al. 2004). Not to spoil the fun, but my lab has also found genome sizes this small in other groups, though these have not yet been published. The largest insect genome size known is found in the mountain grasshopper Podisma pedestris at 16.6 billion base pairs (Westerman et al. 1987).

The smallest eukaryotic genome known to date is that of the protist Encephalitozoon intestinalis, a parasitic microsporidian with a genome size of only 2.3 million base pairs, which is smaller than that of many bacteria (Vivarès and Méténier 2000). The smallest free-living eukaryote genome size is found in Ostreococcus tauri at 12.6 million base pairs (Derelle et al. 2006). The largest reliable protozoan genome size estimate reported to date is 97.8 billion base pairs in the dinoflagellate Gonyaulax polyedra (Shuter et al. 1983). That is a more than 33,000-fold range among protists.

It should be pointed out that the largest published eukaryote genome size estimate is 1,400 billion base pairs (400 times larger than human) in the free-living amoeba Chaos chaos (Friz 1968), although the largest genome size is often attributed to Amoeba dubia at 700 billion base pairs based on the same study. These data are not generally considered reliable, for several reasons. First, these values for amoebae were based on rough biochemical measurements of total cellular DNA content, which probably includes a significant fraction of mitochondrial DNA. Second, Friz’s (1968) value of 300pg for Amoeba proteus is an order of magnitude higher than those reported in subsequent studies (Byers 1986). Third, some amoebae (e.g., A. proteus) contain 500-1000 small chromosomes and are quite possibly highly polyploid (Byers 1986), in which case these values would be inappropriate for a comparison of haploid genome sizes among eukaryotes.

Finally, the smallest genome so far known for any cellular organism also was discovered recently — that of the endosymbiotic bacterium Carsonella ruddii at a miniscule 159,662 base pairs (Nakabachi et al. 2006). This species resides within specialized cells inside the body of psyllid insect hosts. The genome is so small, and the insect and bacterium so mutually dependent, that this species blurs the lines between bacteria and organelles, and probably is similar in some ways to an intermediate stage in the evolution of other obligate intracellular symbionts turned organelles like mitochondria and chloroplasts.

The old assumption, still often repeated, that viruses have smaller genomes than bacteria which have smaller genomes than single-celled eukaryotes which have smaller genomes than multicellular eukaryotes is beginning to wear thin. The pattern remains in a general sense, but focusing only on such a coarse scale overlooks a significant amount of diversity within, and increasingly apparent overlap between, groups of life.

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Readers interested in exploring genome size data can check out the various online databases for more.

References

Byers, T.J. 1986. Molecular biology of DNA in Acanthamoeba, Amoeba, Entamoeba, and Naegleria. International Review of Cytology 99: 311-341.

Derelle, E., C. Ferraz, S. Rombauts, P. Rouzé, A.Z. Worden, S. Robbens, F. Partensky, S. Degroeve, S. Echeynié, R. Cooke, Y. Saeys, J. Wuyts, K. Jabbari, C. Bowler, O. Panaud, B. Piégu, S.G. Ball, J.P. Ral, F.Y. Bouget, G. Piganeau, B. De Baets, A. Picard, M. Delseny, J. Demaille, Y. Van de Peer, H. Moreau. 2006. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proceedings of the National Academy of Sciences of the USA 103: 11647-11652.

Friz, C.T. 1968. The biochemical composition of the free-living amoebae Chaos chaos, Amoeba dubia, and Amoeba proteus. Comparative Biochemistry and Physiology 26: 81-90.

Gregory, T.R. 2005. Synergy between sequence and size in large-scale genomics. Nature Reviews Genetics 6: 699-708.

Gregory, T.R., J.A. Nicol, H. Tamm, B. Kullman, K. Kullman, I.J. Leitch, B.G. Murray, D.F. Kapraun, J. Greilhuber, and M.D. Bennett. 2007. Eukaryotic genome size databases. Nucleic Acids Research 35 (Suppl. 1): D332-D338.

Greilhuber, J., T. Borsch, K. Müller, A. Worberg, S. Porembski, W. Barthlott. 2006. Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size. Plant Biology 8: 770-777.

Johnston, J.S., L.D. Ross, L. Beani, D.P. Hughes, and J. Kathirithamby. Tiny genomes and endoreduplication in Strepsiptera. Insect Molecular Biology 13: 851-585.

Nakabachi A, A. Yamashita, H. Toh, H. Ishikawa, H.E. Dunbar, N.A. Moran, and M. Hattori. 2006. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314: 267.

Raoult, D., B. La Scola, and R. Birtles. 2007. The discovery and characterization of Mimivirus, the largest known virus and putative pneumonia agent. Clinical Infectious Diseases 45: 95-102.

Rees, D.J., F. Dufresne, H. Glémet, and C. Belzile. 2007. Amphipod genome sizes: first estimates for Arctic species reveal genomic giants. Genome 50: 151-158.

Vivarès, C.P. and G. Méténier 2000. Towards the minimal eukaryotic parasitic genome. Current Opinion in Microbiology 3: 463–467.

Westerman, M., N.H. Barton, and G.M. Hewitt (1987). Differences in DNA content between two chromosomal races of the grasshopper Podisma pedestris. Heredity 58: 221-228



5 comments to Genomes large and small.

  • Carl

    Out of curiosity–what about big and small inventories of protein-coding genes? I guess a virus with a couple genes would be at one end, but what about the high end?

    Perhaps with the ever-blurring nature of the gene, that’s not a good question…

      (Quote)

  • Nick (Matzke)

    I think the conventional wisdom is that, at least for multicellular eukaryotes, the critters will have about the *same* number of protein-coding genes, despite the total genome size varying over a range of 2-3,000.

    Which is another reason why news stories of the form “Lab X found some sort of function, or rather effect, for this bit of noncoding DNA” are not particularly convincing.

      (Quote)

  • TR Gregory

    Out of curiosity–what about big and small inventories of protein-coding genes? I guess a virus with a couple genes would be at one end, but what about the high end?

    Perhaps with the ever-blurring nature of the gene, that’s not a good question…

    I suspect that genome size and gene number (defined as protein-coding regions) are closely correlated in viruses as they are in bacteria (but not in eukaryotes and certainly not in animals or plants), though I don’t know enough regarding viruses to say for sure.

    I think the conventional wisdom is that, at least for multicellular eukaryotes, the critters will have about the *same* number of protein-coding genes, despite the total genome size varying over a range of 2-3,000.

    Which is another reason why news stories of the form “Lab X found some sort of function, or rather effect, for this bit of noncoding DNA” are not particularly convincing.

    I suspect that gene numbers are pretty limited relative to genome size. For example, there is a 120-fold divergence in genome size in amphibians, but I doubt that they range from, say, 20,000 to 2,400,000 genes. It’s quite evident that some non-coding DNA is functional, but the onion test rules out any obvious universal function for it all. And indeed, the functions that have been found (or indirectly suggested) apply to small portions of the total (~5%) even in medium-size genomes of humans and mice.

      (Quote)

  • TR Gregory

    I checked the original paper again. “The Mimivirus genome possessed only a very low proportion of noncoding DNA (9.5%) and ~1260 putative open-reading frames ORFs) [i.e., sequences indicative of protein-coding genes]”.

    It seems gene duplication and probably lateral gene transfer (from bacteria and not the amoeba host) are potentially responsible.

    What’s also cool is that the sequences showed similarities to some identified from environmental genomics sampling of the Sargasso Sea, suggesting that similar viruses occur in marine settings.

    The paper is open access here.

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