Turtle Genome Released!

The first paper on the Chrysemys picta genome came out today in Genome Biology. The paper is only the tip of the iceberg in terms of interesting questions that are currently being explored using these data, but it’s satisfying to finally have a paper out on the topic and to have the first genome for a turtle officially released. The sequencing and analyses of this genome have been years in the making, so we’re pretty excited about this here in the lab.

The main findings of the paper relate to the evolution of anoxia tolerance, loss of teeth, as well as the phylogenetic position and rate of evolution of turtles. Note that Genome Biology’s website has mistakenly alphebetized the author list, so we’re all out of order. The correct citation is:

Shaffer, HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela, J Abramyan, D Badenhorst, KK Biggar, GM Borchert, CW Botka, RM Bowden, EL Braun, AM Bronikowski, BG Bruneau, LT Buck, B Capel, TA Castoe, M Czerwinski, KD Delehaunty, SV Edwards, CC Fronick, MK Fujita, L Fulton, TA Graves, RE Green, W Haerty, R Hariharan, LW Hillier, AK Holloway, D Janes, FJ Janzen, C Kandoth, L Kong, APJ de Koning, Y Li, R Literman, SE McGaugh, L Mork, M O’Laughlin, RT Paitz, DD Pollock, CP Ponting, S Radhakrishnan, BJ Raney, JM Richman, J St. John, T Schwartz, A Sethuraman, PQ Spinks, KB Storey, N Thane, T Vinar, LM Zimmerman, WC Warren, ER Mardis, and RK Wilson. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14:R28 doi:10.1186/gb-2013-14-3-r28

I’ve been involved with this project as a member of the organization committee (composed of Brad Shaffer, Andy Shedlock, Nicole Valenzuela, Pat Minx, and myself) from back when we first got approval for sequencing. The initial aim for this set of analyses started developing in a meeting of this committee at the Genome Institute in St. Louis back in December 2010. As often happens, these plans and timelines have shifted a lot. The intervening period has seen the addition of a large number of absolutely awesome, skilled and insightful collaborators, the forging and subsequent dissolution of an international collaborative agreement (yugh…), and dramatic changes to the scientific and funding landscape involving the sequencing of genomes both in the US and worldwide.

The brainstorming notes that started the process of writing this paper back in 2010.

It’s a total personal aside, but my favorite part of this entire project was the short field trip that Phil Spinks and I undertook to catch the “genome turtle” in May 2008. The situation we were in was that we had recently found out that we were funded, were in the queue for sequencing at the Genome Institute, but needed the damn turtle. We frantically threw together some equipment, drove up to Washington, and started jumping in lakes. As far as “challenging field work” goes, it was a pretty low key task – catch an easy to catch turtle, in a place where they are reasonably common, during a time of year that they are very active. It turned out that way too – I caught our first turtle within a few hours of arriving, but it still felt like a lot of pressure at the time. There was concern we would lose our place in the queue (..which wound up happening several times anyway…not for lack of turtle DNA) and that was my first time doing field work that affected something larger than just my dissertation.