Making popcorn for the coming tardigrade wars

tardigrade

This could get interesting. I've seen a lot of stories about this recent paper on the tardigrade genome:

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.

And here are a few of the follow-up stories in the popular press:

The Tardigrade, World's Cutest Microscopic Animal, is Filled with Alien DNA

What the World's Toughest Animal Is Really Made Of

Indestructible 'Water Bears' Have Really Weird Genomes

The authors are saying that about 18% of the tardigrade genome is a product of horizontal gene transfer…that they're full of genes gathered up from bacteria, and that this was adaptive, playing a role in their ability to survive dessication.

I have to say…I had my doubts. That seemed really unlikely, not only that they'd have a history of that much HGT, but that it could be assigned to functional roles. But OK, they published it, let's see how it shakes out.

Here's where it gets interesting: another paper has just come online that says it's all an artifact. Tardigrades are tiny, on the order of a thousand cells, so it's difficult to sample them for sequencing without also picking up lots of bacterial contamination. Here's the abstract:

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.

And their conclusion:

Our assembly, and inferences from it, conflict with a recently published draft genome (UNC) for what is essentially the same strain of H. dujardini. Our assembly, despite having superior assembly statistics, is ~120 Mb shorter than the UNC assembly. Our genome size estimate from sequence assembly is congruent with the values we obtained by direct measurement. We find 15,000 fewer protein-coding genes, and a hugely reduced impact of predicted HGT on gene content in H. dujardini. These HGT candidates await detailed validation. While resolution of the conflict between these assemblies awaits detailed examination based on close scrutiny of the raw UNC data, our analyses suggest that the UNC assembly is compromised by sequences that derive from bacterial contaminants, and that the expanded genome span, additional genes, and HGT candidates are likely to be artefactual.

This could get very interesting.

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