Tardigrades aren’t champion gene swappers after all

A peek at tardigrades’ genetic diaries may dispel a rumor about an amazing feat the tiny creatures were supposed to perform: borrowing large numbers of genes from other organisms.

Tardigrades — also known as water bears and moss piglets — hardly ever borrow DNA from other creatures, researchers report July 27 in PLOS Biology.

New analyses of DNA from two species of water bear, Hypsibius dujardini and Ramazzottius varieornatus, also reveal some of the extreme survival strategies that make the creatures so tough, such as how they produce proteins that allow them to dry out. Dry tardigrades can famously survive extreme temperatures, being bombarded with radiation and even a trip to the vacuum of space. What’s more, some assertions in the study may even reignite debate about tardigrades’ proper place in the tree of life.
These glimpses of tardigrade biology stem in large part from a new detailed reconstruction of H. dujardini’s genome, or complete set of genetic instructions, based on comparisons of three attempts to crack the tardigrade genome. Two of those genomes were assembled by the labs of two of the new study’s coauthors: evolutionary geneticist Mark Blaxter of the University of Edinburgh and molecular biologist Kazuharu Arakawa of Keio University in Kanagawa, Japan. Blaxter and Arakawa compared their teams’ work with a version of the tardigrade genome published by tardigrade biologist Bob Goldstein of the University of North Carolina at Chapel Hill and colleagues.
“The new genome appears to be very accurate and complete,” says Goldstein, who was not involved in the study. “This is a big step toward further understanding these interesting organisms, and toward understanding how life can survive extremes.”
Goldstein’s first draft of the tardigrade genome wasn’t a complete instruction manual. It was chopped in more than 16,175 pieces, typically about 13,000 base pairs long — more like notes on a stack of index cards than a coherent story. Base pairs are the information-carrying chemical units of DNA and are often represented by the letters A, T, C and G. Much of the information contained in that first draft has since proven to be contamination.

The new work is also an incomplete draft, but is more like an anthology of 1,421 genetic short stories, averaging about 73,000 base pairs long. (The longest piece is akin to a novella more than 2.1 million base pairs long, and the shortest is only 1,000 base pairs, the genetic equivalent of a Twitter message.)
Goldstein and colleagues had reported that tardigrades imported about 17 percent of their genes from foreign sources using a type of DNA swapping known as horizontal gene transfer (SN Online: 11/25/15). But Blaxter and colleagues soon called that assertion into question, as their tardigrade genome showed hardly any foreign genes (SN Online: 12/8/15).

After comparing all three genomes, the researchers have now found that tardigrades borrowed only 133 genes, about 0.7 percent of their genes, from other organisms. For multicellular organisms, “that’s about normal,” Blaxter says. “Nothing particularly exciting.”

Having three versions of the genome to compare helped the researchers distinguish between contamination and real horizontal gene transfer, says Max Telford, a phylogeneticist at University College London. “Presumably the contamination would be different in each sample, but the tardigrade DNA would be the same. So that gives you a big clue.”

Even Goldstein is now convinced that tardigrades aren’t super DNA-swappers. “The authors’ analysis methods, and their methods for getting clean DNA, are certainly an improvement over our own earlier methods,” he says.

Some of the new conclusions are more controversial. For instance, the researchers present evidence that tardigrades are close cousins, or a sister group, to worms called nematodes.

“I am not convinced,” says Rosa Fernandez, an evolutionary biologist at the Centre for Genomic Regulation in Barcelona. She says that it has been a recalcitrant question exactly how tardigrades are related to seven other phyla of molting animals known as ecdysozoans, a group that includes both arthropods and nematodes. Because water bears have body segments and multiple legs, they have traditionally been considered close relatives of arthropods, such as spiders.

This study can’t rule out coincidence or other biases in the analysis methods as the reason tardigrades and nematodes appear to be closely related, Fernandez says. She and Telford both think tardigrades belong with arthropods, but, says Telford, “It’s still an open question.”