The curious case of the tardigrade genome.

There has been a lot of interest in tardigrades (aka “water bears”) recently. Not just because they’re very cool, but because they seem to have some very curious genomes. Maybe.

Waterbear

See, in a paper published in PNAS on November 23rd, Boothby et al. (2015) reported evidence of “extensive horizontal gene transfer” in the genome sequence of the tardigrade Hypsibius dujardini. As was widely reported in the science press, this included a lot of foreign DNA in the tardigrade genome, including from very distantly related taxa — plants, fungi, bacteria, you name it. (You may recall that there were initially some claims to this effect about the human genome as well, which did not stand up to subsequent scrutiny).

Boothby et al. (2015) summarized their findings as follows:

Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.

But just today, a preprint made available in BioRxiv by Koutsovoulos et al. (2015) presented a very different analysis of the H. dujardini genome:

Tardigrades are meiofaunal ecdysozoans and are key to understanding the origins of Arthropoda. We present the genome of the tardigrade Hypsibius dujardini, assembled from Illumina paired and mate-pair data. While the raw data indicated extensive contamination with bacteria, presumably from the gut or surface of the animals, careful cleaning generated a clean tardigrade dataset for assembly. We also generated an expressed sequence tag dataset, a Sanger genome survey dataset and used these and Illumina RNA-Seq data for assembly validation and gene prediction. The genome assembly is ~130 Mb in span, has an N50 length of over 50 kb, and an N90 length of 6 kb. We predict 23,031 protein-coding genes in the genome, which is available in a dedicated genome browser at http://www.tardigrades.org. We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.

So, which report is correct? Is the tardigrade genome packed with foreign DNA, or is this likely the result of contamination? I don’t have an answer, but here’s another little curiosity to add to the mix. My lab had previously provided a genome size estimate for this species using both flow cytometry and Feulgen image analysis densitometry, which came out to 1C = 75Mbp (Gabriel et al. 2007).

Here’s the output from the flow cytometry estimate:

12-2-2015 1-07-26 AM

And here you can literally see that there is less DNA in the somatic nuclei of the tardigrade (HD) than in haemocyte nuclei from Drosophila melanogaster (DM) (1C = 175Mbp):

12-2-2015 1-07-57 AM

This estimate differed substantially from what the sequence was indicating, namely a genome more than 200Mbp in length. Given this discrepancy, we were asked to run some more samples of H. dujardini. We used both methods again (albeit with different equipment, as this was a number of years after the initial estimates were done), and got a similar though higher estimate of about 1C = 100Mbp.

TardigradesA

In other words, the sequence seemed to contain twice as much DNA as what we were estimating to be in the nucleus using flow cytometry and image analysis densitometry. We figured that it’s possible that this species undergoes chromatin diminution (deletion of a substantial quantity of DNA during somatic differentiation, such that there is more DNA in the germline than in somatic cells), although this hadn’t previously been documented in tardigrades. Beyond that, it remained a mystery.

It is notable, though, that Koutsovoulos et al. (2015) also obtained an estimate of genome size using flow cytometry (with a different fluorochrome and different standards), and their value was very close to our revised estimate, at 1C = 110Mbp. Their sequence length was also much shorter than in the Boothby et al. (2015) paper, at about 135Mbp.

Boothby et al. (2015) also noted that it is difficult to obtain uncontaminated material from these tiny organisms, and that DNA from their food (bacteria and algae) can end up in even carefully-prepared samples. It therefore seems possible that the large discrepancy between sequence and flow cytometric/densitometric genome size estimates reflects this issue.

Regardless of whether their genomes turn out to be very weird or not, tardigrades are still cool.


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