Water bears’ genetic borrowing questioned

Water bears may not be champion gene borrowers after all, a new analysis suggests.

Researchers in Scotland and colleagues say foreign genes may account for less than 1 percent of the genome of the famously hardy critters, technically known as tardigrades (Hypsibius dujardini). That result, reported in a paper posted online December 1 at BioRxiv.org, directly contradicts a previous study concluding that tardigrades got about 17 percent of their genes from bacteria and other organisms. The earlier study, led by Bob Goldstein at the University of North Carolina at Chapel Hill, was published November 23 in the Proceedings of the National Academy of Sciences (SN Online: 11/25/15).

When researchers in evolutionary biologist Mark Blaxter’s lab at the University of Edinburgh saw the 17 percent claim, they were puzzled. Blaxter and colleagues have been piecing together all the genes that make up tardigrades and have found that the tardigrade genome doesn’t contain many foreign genes at all.

“We said, ‘This is so different from our assembly, something must be wrong,’” Blaxter recalls. Blaxter and colleagues got raw data from Goldstein’s group and compared it with their own version of the water bear genome. The bacterial DNA in the reported tardigrade genome is mostly contamination, not real cases of gene swapping, or horizontal gene transfer, Blaxter’s team reports. About 30 percent of all the DNA in the North Carolina group’s tardigrade genome may be contaminants, the researchers calculate.

Goldstein and coauthor Thomas Boothby said in a written comment that the new analysis “raises some reasonable concerns about contamination in our recent paper. 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.” The researchers say they are examining the data but have declined to comment further.

A few genes really may have been scavenged from other organisms; Blaxter’s group was able to confirm that 54 of the proposed borrowed genes in Goldstein’s group’s analysis are embedded in the tardigrade genome. But that’s far from the more than 6,600 alien genes that Goldstein’s group discovered in the water bear’s genome.

Other scientists who had examined the original report had praised the group’s efforts to rule out contamination as the source of the foreign genes. If Blaxter’s group didn’t have their own water bear genome to compare with the North Carolina version, “we might have raised an eyebrow and said, ‘Wow! Seventeen percent is a lot, but they verified it … so it must be right,’” says Sujai Kumar, who helped analyze the data in Blaxter’s lab.

Only 107 of the alleged foreign genes underwent close scrutiny in the original study. The researchers extrapolated the results to the rest of the genes, but that’s too far of a stretch, says Blaxter.

“Our conclusion is that the Goldstein lab did the right set of tests, but didn’t apply them rigorously enough,” he says.

Steven Salzberg, a computational biologist at Johns Hopkins University, has seen claims of horizontal gene transfer that didn’t pan out before. Salzberg was tipped off that something might be wrong with the tardigrade genome when he read that it contains more than 212 million bases, the information-containing chemical units of DNA. That’s more than twice the size Goldstein’s group had previously reported.

Part of the difficulty in working with tardigrades is that they are so small, containing only about 1,000 cells. Scientists have to pool many of the little animals together to get enough DNA to analyze. “When you do that, you get their microbiomes and you get their food. There’s no way around it,” Salzberg says.

As a result, DNA from the microbiome — the microbes that live in and on the animals — and the algae the tardigrades eat ends up mixed with tardigrade’s own genes. That’s roughly like mixing many million-piece jigsaw puzzles together and then trying to assemble one picture, with no cover photo as a guide. It’s “computationally complex” to say the least, Salzberg says. The tardigrade genome that Goldstein’s group put together is in thousands of small pieces, Salzberg says. Many of those pieces may be partially assembled bacterial genomes that aren’t actually part of the tardigrade puzzle.

Still, it’s not yet established that the Edinburgh analysis is the correct one, says molecular cell biologist Chiara Boschetti of the University of Cambridge. “They may have over-cleaned their data,” removing some real cases of gene swapping.

Such quick testing of extraordinary claims “is how science should work,” Boschetti says. It doesn’t matter who is right. “Let’s find out where the truth is.”