Blair W. Perry, University of Texas at Arlington
Daren C. Card, University of Texas at Arlington
Joel W. McGlothlin, Virginia Tech
Giulia I.M. Pasquesi, University of Texas at Arlington
Richard H. Adams, University of Texas at Arlington
Drew R. Schield, University of Texas at Arlington
Nicole R. Hales, University of Texas at Arlington
Andrew B. Corbin, University of Texas at Arlington
Jeffery P. Demuth, University of Texas at Arlington
Federico G. Hoffmann, Mississippi State University
Michael W. Vandewege, Temple University
Ryan K. Schott, University of Toronto
Nihar Bhattacharyya, University of Toronto
Belinda S.W. Chang, University of Toronto
Nicholas R. Casewell, Liverpool School of Tropical Medicine
Gareth Whiteley, Liverpool School of Tropical Medicine
Jacobo Reyes-Velasco, New York University Abu Dhabi
Stephen P. Mackessy, University of Northern Colorado
Tony Gamble, Marquette University
Kenneth B. Storey, Carleton University
Kyle K. Biggar, Carleton University
Courtney N. Passow, University of Minnesota
Chih-Horng Kuo, Academia Sinica
Suzanne E. McGaugh, University of Minnesota
Anne M. Bronikowski, Iowa State University
A.P. Jason de Koning, University of Calgary
Scott V. Edwards, Harvard University
Michael E. Pfrender, University of Notre Dame
Patrick Minx, Washington University School of Medicine
Edmund D. Brodie Jr., Utah State UniversityFollow
Edmund D. Brodie Jr., Utah State UniversityFollow
Wesley C. Warren, Washington University School of Medicine
Todd A. Castoe, University of Texas at Arlington

Document Type

Article

Journal/Book Title/Conference

Genome Biology and Evolution

Volume

10

Issue

8

Publisher

Oxford University Press

Publication Date

7-30-2018

Creative Commons License

Creative Commons Attribution-Noncommercial 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License

First Page

2110

Last Page

2129

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.

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