Rattlesnake genome published in Genome Research
I am excited to announce our recently-published paper on the Prairie Rattlesnake (Crotalus viridis) genome! In this paper, we describe our work constructing a chromosome-level assembly for this snake, which is one of the only assemblies of this quality for any reptile and the first produced with only Illumina data (to our knowledge). The trick: incorporate cutting-edge genomics techniques like Hi-C. With help from Dovetail Genomics, we were able to go from a scaffold N50 size of around 150 kb to scaffolds that approximate chromosomes in this species.
This was a long-running project in the Castoe lab and I like to think my time toiling with early assembly versions was important in allowing us to produce this resource and the accompanying paper. Drew really pulled everything together in the end, however, with the outstanding Dovetail assembly allowing us to tackle questions we did not even dream of pursuing just a couple years ago. You should read the paper to learn all about it, but we explore a range of research areas encompassing microchromosome biology in reptiles, sex chromosome evolution in vertebrates, and venom gene regulation. You can get a quick summary from the press release produced by UTA. Overall, I think this is a valuable resource for those studying vertebrate genomics and evolution, and I hope that it will motivate others to produce genomic resources for squamate reptiles, which have been largely neglected in recent genome initiatives.
Here is the full citation:
Schield, Drew R., Daren C. Card, Nicole R. Hales, Blair W. Perry, Giulia M. Pasquesi, Heath Blackmon, Richard H. Adams, Andrew B. Corbin, Cara F. Smith, Balan Ramesh, Jeffery P. Demuth, Esther Betrán, Marc Tollis, Jesse M. Meik, Stephen P. Mackessy, and Todd A. Castoe. The Origins and Evolution of Chromosomes, Dosage Compensation, and Mechanisms Underlying Venom Regulation in Snakes. Genome Research 29 (4): 590–601. https://doi.org/10.1101/gr.240952.118.
Photo and graphic from Blair Perry.