A New Analysis Questions How Much Foreign DNA Tardigrades Actually Have
Two research groups sequencing the genome of the same species of ‘water bear’ report different results.
Image: Peter Von Bagh/Flickr
Tardigrades, the teensy "water bears" that can survive outer space, are the weirdest creatures—but some scientists are suggesting they're maybe not quite as genomically unusual as a recent study suggests.
Last month we covered a paper published in PNAS that reported the results of an effort to sequence the tardigrade genome, based out of the University of North Carolina at Chapel Hill. Astoundingly, the study found that around 17.5 percent of the tardigrade genome was comprised of foreign DNA, much more than any other animal sequenced. The researchers suggested this large amount of horizontal gene transfer (HGT)—which is when genes are incorporated into a genome from another organism—could even offer insight into how tardigrades can survive extreme environments.
But another team of scientists that also sequenced the genome of a tardigrade from the same species and strain claims to have found a much lower amount of HGT (around one percent) and suggests in a paper currently in preprint but available on the BioRxiv server that there is "no evidence of massive horizontal gene transfer in [tardigrade species] H. dujardini."
Mark Blaxter, who led the team behind the new preprint paper at the University of Edinburgh, explained in a phone call that his lab thinks the UNC team findings are the result of contamination, and that the foreign bacterial DNA isn't actually part of the tardigrade genome. Blaxter, who was joined on the call by researcher Sujai Kumar, said his team had been in the process of sequencing when the PNAS paper came out.
"We'd held back from publishing our data because we knew we'd found a lot of contamination in the raw data we generated in our genome," Blaxter said. "Basically these little beasties are only up to about half a millimetre long, and it's very hard to scrub them clean." Just as humans come with a bunch of bacteria living in our skin and guts, so do tardigrades.
The researchers of the new paper—which as a preprint has not yet been peer reviewed or accepted for publication—claim that the UNC group got a bigger genome altogether and found more HGT because they didn't clean their data enough to get rid of these bacterial hitchhikers.
"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," they conclude in the paper.
Ed Yong at The Atlantic has a pretty good breakdown of some of the differences in sequencing and data analysis techniques used by the two groups and the genes affected.
The mystery of this most mysterious of minibeasts continues
The authors of the UNC paper did not want to discuss until further analyses are complete. However, in a comment on the preprint page of the Edinburgh group, UNC researchers Thomas Boothby and Bob Goldstein wrote that the contrasting genome sequence paper "raises some reasonable concerns about contamination in our recent paper."
They continued, "We thought seriously about the possibility of contamination—it was of course the most likely initial explanation for the large amount of foreign DNA found in our assembly—and much of the analysis in our paper was designed specifically to address this issue."
And so the mystery of this most mysterious of minibeasts continues.
Blaxter said the researchers are communicating with each other over the issue, and praised the PNAS authors for making their data available quickly. "That's the wonderful thing about connected science, I guess: We do go to sleep sometimes, but somebody's awake somewhere and working on exactly the same project."
Similarly, Boothby and Goldstein said in their comment that they would continue to work on resolving the issues and that "We appreciate that the bioRxiv preprint server is a valuable way to move science like this forward without delay, and we're grateful to [lead author] Koutsovoulos and coauthors for making use of it."
Blaxter emphasised that the Edinburgh researchers were not alleging any malpractice and that this was a good example of scientists working together in the open to reach the correct conclusion. "We think it's actually a victory for new science, this whole process," he said.
And in the future, genome sequencing in particular might be much easier to check and double-check. "As sequencing becomes cheaper and cheaper and better and better, I think it'll be a trivial exercise maybe in three, four, five years time to revisit this question and use some new sequencing technology to re-sequence the tardigrade genome for very little money and just say: this is the truth," said Blaxter.
Meanwhile, I'm standing by my assessment that tardigrades are still the strangest animals, regardless the details of their DNA.