Forum:Genome assembly is hard: the tardigrade genome.

Question

[Istvan Albert]

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
2. The genome of the tardigrade Hypsibius dujardini, BioArxiv

[Istvan Albert]

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/

[poisonAlien]

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

[Istvan Albert]

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/

[5heikki]

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..

[Istvan Albert]

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.

Answer 1

[Istvan Albert]

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