Tardigrade genome sparks controversy
Horizontal gene transfer overestimated for Tardigrades.
Image credit: Phineas Jones, creative commons license (Attribution-NonCommercial-NoDerivs 2.0)
Moss piglets, water bears, whatever you like to call them, Tardigrades are some of the most fascinating critters of the animal kingdom. They are well known for their durability and are often referenced for their ability to survive desiccation and the vacuum of space! Tardigrades recently made some interesting headlines such as “Secrets of the indestructible organism unveiled” and “To kill a mocking Tard” after a draft genome approximated that 1/6 of their genome was acquired by stealing from other species. The paper published by Bob Goldstein’s Lab in PNAS was downloaded over 25,000 times and was picked up by the Washington Post and National Geographic.
Water bears occupy an interesting branch of the tree of life, they are part of Ecdysozoa, which contain two well-studied model organisms Drosophila and C. elegans, but ultimately comprise their own phylum, the Tardigrada. This makes them a fascinating model for studying the evolution of development and a well-sequenced genome is an invaluable tool for this research.
Goldstein estimates that 17.5% of Hypsibius dujardini genes were acquired from horizontal gene transfer, which blows the previous rotifer record holder (less than 10%) out of the water. The vast majority of these genes appeared to be of bacterial origin. The group asserts that this was not due to contamination and made some tenuous claims to back it up such as the water bears were fed algae and not bacteria or that contamination was not likely a problem as no human DNA was found in their reads.
The researchers confirm through PCR that several of the tested bacterial genes were physically linked to the tardigrade’s genes of a metazoan origin. A handful of horizontally transferred gene candidates showed U2-splicesomal introns and had codons that evolved a metazoan bias, which supports their claims. They also compare their genome to other ecdysozoa and noted that there was an expansion of gene families involved in stress response, DNA damage repair, antioxidant pathways, and chaperones. The group hypothesizes that upon rehydration after desiccation tardigrades membranes become leaky and that breakage in their DNA allow them to soak up foreign genetic material like a sponge (a sort of chicken or egg logic)!
However, only one week later Mark Blaxter’s group at Edinburgh rushed to refute the claim by publishing their own genome draft in BioRxiv (archive) a non-peer reviewed repository related to the site commonly used by mathematicians, physicists and computer scientists. They predict a whopping 15,000 fewer genes then Goldstein and their data showed that the horizontal gene transfer claim was grossly overestimated. Blaxter et al. finds that only 36 bacterial-like genes have more than 1,000 RNA-Seq reads. They also claim that the PCR confirmation performed by Goldstein’s group are bacterial pairs and not bacterial-metazoan linked genes. The authors make the important point that most foreign DNA incorporation would be “dead on arrival” because if would have to acquire cis-regulatory sequences or would have to be inserted in frame and thus these sequences would evolve neutrally.
Furthermore, the species studied in each case does not readily enter cryptobiosis, the state responsible for its robustness, a trait that is often erroneously attributed to all tardigrades. Thus we still don’t have insight into how these cute, eight-legged, micro-monsters are able to survive such extreme conditions. Hopefully other tardigrades that do exhibit cryptobiosis will be sequenced in the future, allowing for genomic comparisons that will shed light on how water bears can survive a trip on a satellite in outer space.
Boothby et al. (2015) PNAS. 112 (52) 15976-15981.
Koutsovoulos et al. (2015) RioRxiv. DOI: http://dx.doi.org/10.1101/033464.