This could get interesting. I’ve seen a lot of stories about this recent paper on the tardigrade genome:
Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.
And here are a few of the follow-up stories in the popular press:
The Tardigrade, World’s Cutest Microscopic Animal, is Filled with Alien DNA
What the World’s Toughest Animal Is Really Made Of
Indestructible ‘Water Bears’ Have Really Weird Genomes
The authors are saying that about 18% of the tardigrade genome is a product of horizontal gene transfer…that they’re full of genes gathered up from bacteria, and that this was adaptive, playing a role in their ability to survive desiccation.
I have to say…I had my doubts. That seemed really unlikely, not only that they’d have a history of that much HGT, but that it could be assigned to functional roles. But OK, they published it, let’s see how it shakes out.
Here’s where it gets interesting: another paper has just come online that says it’s all an artifact. Tardigrades are tiny, on the order of a thousand cells, so it’s difficult to sample them for sequencing without also picking up lots of bacterial contamination. Here’s the abstract:
Tardigrades are meiofaunal ecdysozoans and are key to understanding the origins of Arthropoda. We present the genome of the tardigrade Hypsibius dujardini, assembled from Illumina paired and mate-pair data. While the raw data indicated extensive contamination with bacteria, presumably from the gut or surface of the animals, careful cleaning generated a clean tardigrade dataset for assembly. We also generated an expressed sequence tag dataset, a Sanger genome survey dataset and used these and Illumina RNA-Seq data for assembly validation and gene prediction. The genome assembly is ~130 Mb in span, has an N50 length of over 50 kb, and an N90 length of 6 kb. We predict 23,031 protein-coding genes in the genome, which is available in a dedicated genome browser at http://www.tardigrades.org. We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.
And their conclusion:
Our assembly, and inferences from it, conflict with a recently published draft genome (UNC) for what is essentially the same strain of H. dujardini. Our assembly, despite having superior assembly statistics, is ~120 Mb shorter than the UNC assembly. Our genome size estimate from sequence assembly is congruent with the values we obtained by direct measurement. We find 15,000 fewer protein-coding genes, and a hugely reduced impact of predicted HGT on gene content in H. dujardini. These HGT candidates await detailed validation. 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.
This could get very interesting.
Dang, and here I already shared an article from ScienceAlert boasting about the HGT. Good thing you have the blog on ScienceBlogs I can also share without too much concern I’ll lose clients over linking to an out-spoken atheist lefty blog. Do keep us appraised on the tardigrade wars. They’re fascinating creatures.
….isn’t that almost certainly backwards?
They’re probably all gay.
Interesting!
There was a paper a while back which made a similar claim (of horizontal gene transfer from many different organisms) in bdelloid rotifers.
• Massive Horizontal Gene Transfer in Bdelloid Rotifers (PDF)
Bdelloid rotifers have adaptations that are similar to tardigrades, in that they can survive dessication and other damaging phenomena. I don’t think they’re as tough as tardigrades, but I don’t recall the details.
Hm. Here are more recent papers on the topic:
• Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats
• Foreign genes and novel hydrophilic protein genes participate in the desiccation response of the bdelloid rotifer Adineta ricciae
It certainly looks like no-one has suggested contamination in the above situation.
A related fact that I thought was interesting was the explanation of why some organisms (including tardigrades) are resistant to radiation damage. It was something I wondered about after hearing about it — after all, isn’t it only in recent times (leaving aside the Oklo “reactor” that shut down about 1Gya) that enough purified radiation emitters have been around to potentially affect organisms and their evolution? But the answer, of course, is that dessication damages DNA, and ionizing radiation damages DNA. Those organisms that have evolved to cope with the former have the DNA repair traits necessary to cope with the latter.
‘desiccation’ may be the most misspelled word in environmental biology.
what’s more embarrassing than publishing results from sample contamination?
Well, shit.
Firefox spool chocker does not flag “dessication”.
I was really looking forward to the Tardigrade Wars, but then it turns out it’s not the tardigrades that are doing battle, but academics. Curses!
A battle between tardigrades and academics would be fun, too, although I’m not sure who I’d put my money on.
I was a little worried about Tardigrade Wars – I think I’ve seem those little buggers moving and eating while in a vacuum and being showered with electrons. Scary!
Because tardigrades can effectively completely “dry out” and then later rehydrate, the authors are proposing that during that rehydration, when the structure of the creature is a bit “leaky”, they will tend to suck in foreign unicellular organisms as well as water, and that once inside the creature, these sources of DNA could be easily incorporated into the tardigrades as it repairs its DNA that was fragmented from the dehydration.
So in this particular case, it is indeed features of its ability to survive desiccation that make it more likely to incorporate foreign DNA into its genome. I very much doubt, however, that a blanket statement can be made for all animals that survive extremes.
Apparently, misspelling a word?
Aw man, so many questions. How do / can you sample DNA from these guys? Toss them in a (tiny) blender? A tardigrade is only about a thousand cells? Seems like one thousand is awfully small for anything that “is alive”.
I was going to give tardigrades out as Christmas presents to my friends (wrapped in a bit of moss) but if they’re engaged in a war, I should probably wait for someone to win.
“Seems like one thousand is awfully small for anything that “is alive”.”
Most things that are alive have only one cell.
I love that science is self-correcting. It is OK to be found ‘wrong’ once in a while. Embarrassing, if truly just contamination.
Tardigrades are tiny, on the order of a thousand cells…
So each of the “toes” in the above picture is ~1 single cell? Or a single cell constitutes multiple “toes”?
*sigh*
Yet another beautiful theory killed by a nasty, ugly little fact!
Other recent astonishing claims that turn out to be contamination: arsenic-based life, T. Rex tissue.
I always wanted to return as a Great Canada Goose in a next life, but I’ve changed my mind. Tardigrades are way cooler.
Is there really much chance of a prolonged war here? Contamination is a very straightforward explanation for how one lab can see HGT where another lab does not. I’m having a more difficult time coming up with a scenario in which one lab mistakenly fails to find exactly the DNA that looks like HGT in another lab’s work.
Yeah, if simply cleaning the animals gets rid of the purported HGT sequences in the data set, then it’s hard to explain how this wasn’t contamination. Unless someone wants to argue that the cleaning procedure selectively destroyed genomic DNA.
Interestingly, there is a comment left by the lead author and PI of the first paper on the website of the second paper in which they say, basically, that they were aware of the possibility of contamination and tried hard to account for it. But they appreciate the results of the new paper and are going to proceed with some additional analyses to try to figure it all out.
This does not smack of a “war”. In fact, it seems to be a collegial attempt at getting to the truth of the matter. Let’s hope that this works out exactly as science is supposed to work.
Ooh, tardigrades and cephalopods. Is this the coolest blog ever?
Let’s toss a few dozen of each outside the International Space Station for 24 hours and see. I’d suggest a few subjects from the Discovery Institute, but then I realized that would insult both academics and tardigrades.