The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Genome Biology

Richard K Wilson^2,22  Elaine R Mardis^2,22  Wesley C Warren^2,22  Laura M Zimmerman⁶  Tomas Vinar^2,23  Nay Thane^2,22  Kenneth B Storey⁴  Phillip Q Spinks^1,12  Arun Sethuraman^1,10  Tonia Schwartz^1,10  John St John^2,20  Joy M Richman⁹  Brian J Raney^1,11  Srihari Radhakrishnan^1,10  Chris P Ponting^1,18  David D Pollock²  Ryan T Paitz⁶  Michelle O'Laughlin^2,22  Lindsey Mork^2,26  Suzanne E McGaugh^1,16  Robert Literman^1,10  Yang Li^1,18  AP Jason de Koning²  Lesheng Kong^1,18  Cyriac Kandoth^2,22  Fredric J Janzen^1,10  Daniel Janes^1,10  Alisha K Holloway^1,19  LaDeana W Hillier^2,22  Omar Hernandez⁷  Ramkumar Hariharan^1,17  Wilfried Haerty^1,18  Richard E Green^2,20  Tina A Graves^2,22  Lucinda Fulton^2,22  Matthew K Fujita^2,25  Catrina C Fronick^2,22  Scott V Edwards¹  Kim D Delehaunty^2,22  Mike Czerwinski^2,26  Todd A Castoe^1,15  Blanche Capel^2,26  Leslie T Buck^2,28  Benoit G Bruneau^1,14  Anne M Bronikowski^1,10  Edward L Braun^1,13  Rachel M Bowden⁶  Christopher W Botka³  Glen M Borchert⁵  Kyle K Biggar⁴  Daleen Badenhorst^1,10  Chris T Amemiya^2,27  John Abramyan⁹  Nicole Valenzuela^1,10  Robert C Thomson^2,21  Andrew M Shedlock⁸  Daniel E Warren^2,24  Patrick Minx^2,22  H Bradley Shaffer^1,12 

[1] Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA;Research Computing, Harvard Medical School, Boston, MA 02115, USA;Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada;Department of Biological Sciences, Life Sciences Building, University of South Alabama, Mobile, AL 36688-0002, USA;School of Biological Sciences, Illinois State University, Normal, IL 61790, USA;FUDECI, Fundación para el Desarrollo de las Ciencias Físicas, Matemáticas y Naturales. Av, Universidad, Bolsa a San Francisco, Palacio de Las Academias, Caracas, Venezuela;Medical University of South Carolina College of Graduate Studies and Center for Marine Biomedicine and Environmental Sciences, Charleston, SC 29412, USA;Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada;Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA;Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA;La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA;Department of Biology, University of Florida, Gainesville, FL 32611 USA;Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA;Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA;Biology Department, Duke University, Durham, NC 27708, US;Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud P.O, Thiruvananthapuram, Kerala 695014, India;MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK;Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA;Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA;Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA;The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA;Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia;Department of Biology, Saint Louis University, St Louis, MO 63103, USA;Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA;Benaroya Research Institute at Virginia Mason, Seattle, WA 98101 USA;Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5, Canada

关键词: evolutionary rates;    turtle;    physiology;    phylogenomics;    longevity;    genomics;    freeze tolerance;    chelonian;    anoxia tolerance;    Amniote phylogeny;   

Others  :  866871
DOI  :  10.1186/gb-2013-14-3-r28

 received in 2012-10-18, accepted in 2013-03-28,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Shaffer et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 2.

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