TY - JOUR
T1 - The Burmese python genome reveals the molecular basis for extreme adaptation in snakes
AU - Castoe, Todd A.
AU - De Koning, A. P.Jason
AU - Hall, Kathryn T.
AU - Card, Daren C.
AU - Schield, Drew R.
AU - Fujita, Matthew K.
AU - Ruggiero, Robert P.
AU - Degner, Jack F.
AU - Daza, Juan M.
AU - Gu, Wanjun
AU - Reyes-Velasco, Jacobo
AU - Shaney, Kyle J.
AU - Castoe, Jill M.
AU - Fox, Samuel E.
AU - Poole, Alex W.
AU - Polanco, Daniel
AU - Dobry, Jason
AU - Vandewege, Michael W.
AU - Li, Qing
AU - Schott, Ryan K.
AU - Kapusta, Aurélie
AU - Minx, Patrick
AU - Feschotte, Cédric
AU - Uetz, Peter
AU - Ray, David A.
AU - Hoffmann, Federico G.
AU - Bogden, Robert
AU - Smith, Eric N.
AU - Chang, Belinda S.W.
AU - Vonk, Freek J.
AU - Casewell, Nicholas R.
AU - Henkel, Christiaan V.
AU - Richardson, Michael K.
AU - Mackessy, Stephen P.
AU - Bronikowsi, Anne M.
AU - Yandell, Mark
AU - Warren, Wesley C.
AU - Secor, Stephen M.
AU - Pollock, David D.
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013/12/17
Y1 - 2013/12/17
N2 - Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.
AB - Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.
KW - Comparative genomics
KW - Physiological remodeling
KW - Systems biology
KW - Transcriptomics
KW - Transposable elements
UR - http://www.scopus.com/inward/record.url?scp=84890812848&partnerID=8YFLogxK
U2 - 10.1073/pnas.1314475110
DO - 10.1073/pnas.1314475110
M3 - Article
AN - SCOPUS:84890812848
VL - 110
SP - 20645
EP - 20650
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
IS - 51
ER -