About a week ago I discussed a new paper by Boothby et al. in the Proceedings of the National Academy of Sciences (US) with a stunning finding: the sequenced DNA of the tardigrade species Hypsibius dujardini showed that about 17% of its genome comprised sequences taken from distantly-related species—mostly bacteria. This was the most pervasive example of horizontal gene transfer (HGT) known in animals, though bacteria often have such high levels of HGT.
But maybe that conclusion was premature—or wrong. A new manuscript by Georgios Koutsovoulos et al. (reference and free download at bottom), posted at the website bioRχiv, suggesst that Boothby et al.’s results may have been due to contamination of their DNA sample with bacteria, and the level of HGT in this species may be much lower.
Do be aware, when evaluating the discrepancy between the two papers, that the Koutsovoulos et al. manuscript hasn’t been refereed: the authors simply posted a manuscript—presumably submitted to some unspecified journal—on a public website. But let’s compare them anyway.
Although Boothby et al. argued that they cleaned up their sample to eliminate contamination, Koutovoulos seem to have taken more stringent precautions. And the sequencing of their sample, compared to the published sequences of Boothby et al., showed a very different result. First, about 30% of Boothby’s DNA appears to represent contaminant material.
Granted, their sample was a different isolate of the species (started from one asexually-reproducing female), but their culture and that of Boothby et al. were separated by only fifteen years of divergence, so it’s unlikely that the differences in DNA content result from different genetic constitution of the isolates.
How much of the tardigrade genome is still composed of foreign DNA in the new species? We don’t know completely, but Koutsovolos et al. report that they looked at 23,021 protein-coding genes in the H. dujardini genome, and found only 36 genes that appeared to have a bacterial origin. That’s a proportion of only 0.16%—a far cry from 17%.
Koutsovoulos et al. also note that H. duardini is not known to undergo the drying and rehydration process known as cryptobiosis—a process that takes in lots of water from the environment, destabilizes membranes, and breaks DNA: an idea way to take foreign DNA into your genome. But if this tardigrade doesn’t do that—and I don’t recall Boothby et al. mentioning this fact, though they might have—then it makes it even less likely that the 17% HGT figure is correct.
As I said, the “replication” study hasn’t yet been published after peer review, so we’ll have to suspend judgment. Resolution of this problem will await the publication of the Koutsovoulos et al. paper, and, ideally, a third study (perhaps by Boothby et al.) with very stringent precautions. After all, the press had a field day with the 17% HGT figure, which truly was astounding; and, as Hitchens said, extraordinary claims demand extraordinary evidence.
And a postscript: the methods of both papers are above my pay grade, so read both if you’re in the field and want to judge the results.
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