This week’s discussion is different. But it’s a neat look at the issues of genome assembly, contamination, over-prediction and under-prediction. If you haven’t been following the drama, it began with the paper covered in this story by Ed Yong: Inside the Bizarre Genome of the World’s Toughest Animal. This group suggested that upwards of 17% of the tardigrade genome was imported from other species via horizontal gene transfer (HGT). Then another group who had been working on this species provided their pre-print on their work that came to a very different conclusion. Ed then wrote about that here: Rival Scientists Cast Doubt Upon Recent Discovery About Invincible Animals. They found much lower HGT.
Anyway, this week’s highlighted item from Reddit offers a look one researcher’s take on the whole thing, that comes to a third option.
Quick Look at the Two Manuscripts on Tardigrade LGT (igs.umaryland.edu)
submitted 4 days ago by rs4481887
This links to a blog post by Dr. Julie Dunning Hotopp. She’s worked extensively in lateral gene transfer, and has some excellent commentary on the whole thing. And there’s good discussion in the comments. It sounds to me that she’s suggesting there’s a porridge somewhere that’s just right. One of these was too hot, one was too cold.
It has been a fascinating story or publication, data access, analysis strategies, and gene transfer. I’m including the links to both papers below as well.
Boothby, T., Tenlen, J., Smith, F., Wang, J., Patanella, K., Osborne Nishimura, E., Tintori, S., Li, Q., Jones, C., Yandell, M., Messina, D., Glasscock, J., & Goldstein, B. (2015). Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1510461112
Georgios Koutsovoulos, Sujai Kumar, Dominik R Laetsch, Lewis Stevens, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Aziz Aboobaker, & Mark Blaxter (2015). The genome of the tardigrade Hypsibius dujardini bioRxiv DOI: 10.1101/033464