New Research In
Physical Sciences
Social Sciences
Featured Portals
Articles by Topic
Biological Sciences
Featured Portals
Articles by Topic
- Agricultural Sciences
- Anthropology
- Applied Biological Sciences
- Biochemistry
- Biophysics and Computational Biology
- Cell Biology
- Developmental Biology
- Ecology
- Environmental Sciences
- Evolution
- Genetics
- Immunology and Inflammation
- Medical Sciences
- Microbiology
- Neuroscience
- Pharmacology
- Physiology
- Plant Biology
- Population Biology
- Psychological and Cognitive Sciences
- Sustainability Science
- Systems Biology
The Burmese python genome reveals the molecular basis for extreme adaptation in snakes
Edited by David B. Wake, University of California, Berkeley, CA, and approved November 4, 2013 (received for review July 31, 2013)
This article has a Correction. Please see:
See related content:
- King cobra genome and snake venom evolution- Dec 02, 2013

Significance
The molecular basis of morphological and physiological adaptations in snakes is largely unknown. Here, we study these phenotypes using the genome of the Burmese python (Python molurus bivittatus), a model for extreme phenotypic plasticity and metabolic adaptation. We discovered massive rapid changes in gene expression that coordinate major changes in organ size and function after feeding. Many significantly responsive genes are associated with metabolism, development, and mammalian diseases. A striking number of genes experienced positive selection in ancestral snakes. Such genes were related to metabolism, development, lungs, eyes, heart, kidney, and skeletal structure—all highly modified features in snakes. Snake phenotypic novelty seems to be driven by the system-wide coordination of protein adaptation, gene expression, and changes in genome structure.
Abstract
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.
Footnotes
- ↵1To whom correspondence should be addressed. E-mail: david.pollock{at}ucdenver.edu.
Author contributions: T.A.C. and D.D.P. designed research; T.A.C., A.P.J.d.K., K.T.H., D.C.C., D.R.S., M.K.F., R.P.R., J.F.D., J.M.D., W.G., J.R.-V., K.J.S., J.M.C., S.E.F., A.W.P., D.P., M.W.V., Q.L., R.K.S., A.K., P.M., P.U., E.N.S., B.S.W.C., F.J.V., N.R.C., C.V.H., M.K.R., S.P.M., M.Y., W.C.W., and S.M.S. performed research; T.A.C., J.D., P.M., R.B., E.N.S., A.M.B., W.C.W., S.M.S., and D.D.P. contributed new reagents/analytic tools; T.A.C., A.P.J.d.K., K.T.H., D.C.C., D.R.S., M.K.F., R.P.R., J.F.D., J.M.D., W.G., J.R.-V., K.J.S., S.E.F., M.W.V., Q.L., R.K.S., A.K., P.M., C.F., D.A.R., F.G.H., B.S.W.C., F.J.V., N.R.C., C.V.H., M.K.R., S.P.M., M.Y., W.C.W., S.M.S., and D.D.P. analyzed data; and T.A.C. and D.D.P. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. AEQU00000000).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1314475110/-/DCSupplemental.