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The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Genome Biology
  • H. Bradley Shaffer, University of California, Los Angeles
  • Patrick Minx, Washington University School of Medicine in St. Louis
  • Daniel E. Warren, Saint Louis University
  • Andrew M. Shedlock, College of Charleston
  • Robert C. Thomson, University of Hawaii at Manoa
  • Nicole M. Valenzuela, Iowa State University
  • John Abramyan, University of British Columbia
  • Chris T. Amemiya, Benaroya Research Institute at Virginia Mason
  • Daleen Badenhorst, Iowa State University
  • Kyle K. Biggar, Carleton University
  • Glen M. Borchert, Illinois State University
  • Christopher W. Botka, Harvard Medical School
  • Rachel M. Bowden, Illinois State University
  • Edward L. Braun, University of Florida
  • Anne M. Bronikowski, Iowa State University
  • Benoit G. Bruneau, University of California, San Francisco
  • Leslie T. Buck, University of Toronto, Toronto, Canada
  • Blanche Capel, Duke University
  • Todd A. Castoe, University of Colorado
  • Mike Czerwinski, Duke University
  • Kim D. Delehaunty, Washington University School of Medicine in St. Louis
  • Scott V. Edwards, Harvard University
  • Catrina C. Fronick, Washington University School of Medicine in St. Louis
  • Matthew K. Fujita, University of Texas at Arlington
  • Lucinda Fulton, Washington University School of Medicine in St. Louis
  • Tina A. Graves, Washington University School of Medicine in St. Louis
  • Richard E. Green, University of California, Santa Cruz
  • Wilfried Haerty, University of Oxford
  • Ramkumar Hariharan, Rajiv Gandhi Centre for Biotechnology
  • Omar Hernandez, Fundación Para el Desarrollo de las Ciencias Físicas, Matemáticas y Naturale
  • LaDeana W. Hillier, Washington University School of Medicine in St. Louis
  • Alisha K. Holloway, Gladstone Institute of Cardiovascular Disease
  • Daniel Janes, Iowa State University
  • Fredric J. Janzen, Iowa State University
  • Cyriac Kandoth, Washington University School of Medicine in St. Louis
  • Lesheng Kong, University of Oxford
  • AP Jason de Koning, University of Colorado
  • Yang Li, University of Oxford, UK
  • Robert A. Literman, Iowa State University
  • Suzanne E. McGaugh, Duke University
  • Lindsey Mork, Duke University
  • Michelle O'Laughlin, Washington University School of Medicine in St. Louis
  • Ryan T. Paitz, Illinois State University
  • David D. Pollock, University of Colorado
  • Chris P. Ponting, University of Oxford
  • Srihari Radhakrishnan, Iowa State University
  • Brian J. Raney, University of California, Santa Cruz
  • Joy M. Richman, University of British Columbia
  • John St. John, University of California, Santa Cruz
  • Tonia Sue Schwartz, Iowa State University
  • Arun Sethuraman, Iowa State University
  • Phillip Q. Spinks, University of California, Los Angeles
  • Kenneth B. Storey, Carleton University
  • Nay Thane, Washington University School of Medicine in St. Louis
  • Tomas Vinar, Comenius University
  • Laura M. Zimmerman, Illinois State University
  • Wesley C. Warren, Washington University School of Medicine in St. Louis
  • Elaine R. Mardis, Washington University School of Medicine in St. Louis
  • Richard K. Wilson, Washington University School of Medicine in St. Louis
Document Type
Article
Publication Version
Published Version
Publication Date
1-1-2013
DOI
10.1186/gb-2013-14-3-r28
Abstract
Abstract Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species’ physiological capacities to withstand extreme anoxia and tissue freezing. Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle’s extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders. Keywords: Amniote phylogeny, anoxia tolerance, chelonian, freeze tolerance, genomics, longevity, phylogenomics, physiology, turtle, evolutionary rates
Comments

This is an article from Genome Biology 14 (2013): 1, doi:10.1186/gb-2013-14-3-r28. Posted with permission.

Rights
This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
Shaffer et al
Language
en
File Format
application/pdf
Citation Information
H. Bradley Shaffer, Patrick Minx, Daniel E. Warren, Andrew M. Shedlock, et al.. "The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage" Genome Biology Vol. 14 Iss. R28 (2013) p. 1 - 22
Available at: http://works.bepress.com/fredric-janzen/5/