Tag Archives: horizontal gene transfer

SNPpets_2

Friday SNPpets

This Friday includes a range of topics, as usual. Interesting assessments of the state of autism genomic architecture–and read the piece on the “ghettoization” of genetic disease after that (Laura Hercher’s tweet). Horizontal gene transfer in cheese bacteria. Traits in crops. CRISPR for insects. Deep time in human DNA, and evolutionary history of tumors. There are so many great things around right now…. Off we go!


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


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What’s the Answer? (what’s up with the tardigrades?)

reddit_iconThis 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.

academic_reddit 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.

References:

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