Document Type
Article
Language
eng
Publication Date
8-1-2018
Publisher
Oxford University Press
Source Publication
Genome Biology and Evolution
Source ISSN
1759-6653
Abstract
Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Recommended Citation
Perry, Perry W.; Card, Daren C.; McGlothlin, Joel W.; Pasquesi, Giulia I.M.; Adams, Richard H.; Schield, Drew R.; Hales, Nicole R.; Corbin, Andrew B.; Demuth, Jeffery P.; Hoffmann, Federico G.; Vandewege, Michael W.; Schott, Ryan K.; Bhattacharyya, Nihar; Chang, Belinda S.W.; Casewell, Nicholas R.; Whiteley, Gareth; Reyes-Velasco, Jacobo; Mackessy, Stephen P.; Gamble, Tony; Storey, Kenneth B.; Biggar, Kyle K.; Passow, Courtney N.; Kuo, Chih-Horng; McGaugh, Suzanne E.; Bronikowski, Anne M.; De Konig, A.P. Jason; Edwards, Scott V.; Pfrender, Michael E.; Minx, Patrick; Brodie, Edmund D. III; Brodie, Edmund D. Jr.; Warren, Wesley C.; and Castoe, Todd A., "Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome" (2018). Biological Sciences Faculty Research and Publications. 676.
https://epublications.marquette.edu/bio_fac/676
Comments
Published version. Genome Biology and Evolution, Vol. 10 No. 8 (August 2018): 2110-2129. DOI. © 2018 Oxford University Press. Used with permission. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com