Have the tardigrades been slandered?

Alexander Ershov, N+1 

Biologists led by Mark Blaxter from the University of Edinburgh have discovered that the massive borrowing of foreign genes, traces of which were recently allegedly found in the genome of slow walkers, may actually be the result of pollution. This is stated in a preprint posted by British scientists in the bioArxiv archive (Koutsovoulos et al., The genome of the tardigrade Hypsibius dujardini). 

The article by Mark Blaxter's group has not yet been accepted for publication in any of the peer-reviewed journals and, according to the authors, has not even been fully completed. Nevertheless, the lead author of the American group that discovered "gene theft" has already admitted in a comment to the preprint that the new data call into question the results obtained earlier.

In the new work, British biologists worked with a slow-moving bird of the same species as the Americans, Hypsibius dujardini, but they grew them in slightly different conditions. In addition, since these tardigrades reproduce by parthenogenesis, that is, they are actually clones, the "strain" with which the British worked could differ slightly in its genetic characteristics from the American one. 

British scientists were able to read and assemble the complete genome of slow walkers, the length of which was 135 million base pairs – which is 77 million less than the genome collected by the American group. The number of protein-coding genes was also significantly lower: 23 versus 38 thousand. The main result was the absence of traces of any significant horizontal gene transfer. This is the name of the process during which foreign sequences, for example, viral genes, enter the genome.

According to the American group, the share of borrowed genes in slow walkers is allegedly about 17.5 percent – this is a record figure among all animals. In rotifers, modern record holders for horizontal transport (animals significantly smaller and primitive), the corresponding figure is two times lower. Usually, the proportion of foreign genes in animal genomes is at the level of one percent, and the vast majority of these genes are introduced by viruses. Interestingly, among the sources of the "stolen" genes, the American group found not only bacteria, but also fungi, archaea and even plants.

Diagram of scaffolds (collected pieces) of the American genome of slow walkers by nucleotide composition (horizontal) and number of readings (vertical). Blue shows scaffolds where the same sequence is read not only by DNA, but also by RNA – that is, transcribed. The size of the bubble corresponds to the length of the scaffold.

Of all these genes, the British group experimentally (using a PCR test) managed to confirm the presence of only ten pieces, whose "foreignness" cannot be rejected as contamination. Based on the analysis of their own and other people's raw data, the British estimate the total level of possible contamination for the American genome at 30.4 percent, for their own – at 6.8 percent.

American biologists in their article suggested that it was the high level of horizontal transfer that could help the slow-walkers become so specialized extremophiles. It is known, for example, that they can withstand complete drying, starvation, prolonged ionizing radiation and, for example, are the only animals capable of living in outer space for several days (and in the vacuum of an electron microscope). However, new data cast doubt on the hypothesis that all these "superpowers" are somehow connected with borrowing someone else's DNA. In addition, the authors of the new article emphasize that the species of slow walkers that both groups sequenced, Hypsibius dujardini, does not have these abilities – unlike its other brethren, the total number of which is approaching 1000 species.

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03.12.2015