Forum: Genome assembly is hard: the tardigrade genome.
13
gravatar for Istvan Albert
2.8 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

Here is an interesting development that might be of interest to all bioinformaticians. Two radically different genomes have been assembled for the tardigrade. The authors of the the second paper believe that the results of the first are solely due to contamination.

A bioinformatician's worst nightmare is to wake up and realize that in that in a published analysis of yours something went awfully wrong. It could happen to us all.

1. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade, PNAS, Nov 23, 2015

http://www.pnas.org/content/early/2015/11/18/1510461112.abstract

2. The genome of the tardigrade Hypsibius dujardini, BioArxiv

http://biorxiv.org/content/early/2015/12/01/033464

 

forum assembly • 1.4k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Istvan Albert ♦♦ 77k
2

A nice summary can be found here:

Quick Look at the Two Manuscripts on Tardigrade LGT

http://www.igs.umaryland.edu/labs/hotopp/2015/12/05/quick-look-at-the-two-manuscripts-on-tardigrade-lgt/

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 77k

Here is more on the issue. Rival Scientists Cast Doubt Upon Recent Discovery About Invincible Animals

ADD REPLYlink written 2.8 years ago by poisonAlien2.6k

Another related article:

Inside the Bizarre Genome of the World’s Toughest Animal

http://www.theatlantic.com/science/archive/2015/11/tardigrades-worlds-toughest-animals-borrowed-a-sixth-of-their-dna-from-microbes/417243/

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 77k

Funny how they made HGT the main plot in their story and then didn't really assess thoroughly (almost at all?) if it was real or just contamination. But yeah, quite a nightmare for the lead/corresponding authors..

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by 5heikki7.6k

Yes it could be a sort of a "group think".  Once there was reason to believe that HGT might explain every oddity about this organism no one wanted to really question the very basis of that.

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 77k
4
gravatar for Istvan Albert
2.8 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

Github repository for the BioArxiv paper. This is how science should work. Publish and show the actual code for it. Kudos to the authors.

Scripts and relevant processed data files for Boothby et al 2015 and Koutsovoulos et al 2015 tardigrade genome papers

https://github.com/sujaikumar/tardigrade

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Istvan Albert ♦♦ 77k
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