TY - JOUR
T1 - Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome
AU - Perry, Blair W.
AU - Card, Daren C.
AU - Mcglothlin, Joel W.
AU - Pasquesi, Giulia I.M.
AU - Adams, Richard H.
AU - Schield, Drew R.
AU - Hales, Nicole R.
AU - Corbin, Andrew B.
AU - Demuth, Jeffery P.
AU - Hoffmann, Federico G.
AU - Vandewege, Michael W.
AU - Schott, Ryan K.
AU - Bhattacharyya, Nihar
AU - Chang, Belinda S.W.
AU - Casewell, Nicholas R.
AU - Whiteley, Gareth
AU - Reyes-Velasco, Jacobo
AU - Mackessy, Stephen P.
AU - Gamble, Tony
AU - Storey, Kenneth B.
AU - Biggar, Kyle K.
AU - Passow, Courtney
AU - Kuo, Chih Horng
AU - McGaugh, Suzanne E
AU - Bronikowski, Anne M.
AU - De Koning, A. P.Jason
AU - Edwards, Scott V.
AU - Pfrender, Michael E.
AU - Minx, Patrick
AU - Brodie, Edmund D.
AU - Brodie, Edmund D.
AU - Warren, Wesley C.
AU - Castoe, Todd A.
N1 - Publisher Copyright:
© The Author(s) 2018.
PY - 2018/8/1
Y1 - 2018/8/1
N2 - Colubridae represents themost phenotypically diverse and speciose family of snakes, yet nowell-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 genomestructure that provide insight into the evolution of amniote genomes.Analyses of the garter snake andother squamate reptile genomes highlight shifts in repeat element abundance andexpansionwithin snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z andW 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 evolutionaryorigins ina rear-fanged colubridsnake, togetherwith newgenomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.
AB - Colubridae represents themost phenotypically diverse and speciose family of snakes, yet nowell-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 genomestructure that provide insight into the evolution of amniote genomes.Analyses of the garter snake andother squamate reptile genomes highlight shifts in repeat element abundance andexpansionwithin snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z andW 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 evolutionaryorigins ina rear-fanged colubridsnake, togetherwith newgenomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.
KW - Co-evolution
KW - Sex chromosomes
KW - Thamnophis sirtalis
KW - Venom
KW - Vision
UR - http://www.scopus.com/inward/record.url?scp=85054437212&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85054437212&partnerID=8YFLogxK
U2 - 10.1093/gbe/evy157
DO - 10.1093/gbe/evy157
M3 - Article
C2 - 30060036
AN - SCOPUS:85054437212
SN - 1759-6653
VL - 10
SP - 2110
EP - 2129
JO - Genome biology and evolution
JF - Genome biology and evolution
IS - 8
ER -