Journal article
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
Science (American Association for the Advancement of Science), Vol.346(6215), 1254449
12/12/2014
DOI: 10.1126/science.1254449
PMCID: PMC4386873
PMID: 25504731
Abstract
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
Details
- Title: Subtitle
- Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
- Creators
- Richard E Green - Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.eduEdward L Braun - Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USAJoel Armstrong - Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USADent Earl - Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USANgan Nguyen - Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USAGlenn Hickey - Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USAMichael W Vandewege - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USAJohn A St John - Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USASalvador Capella-Gutiérrez - Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, SpainTodd A Castoe - Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Department of Biology, University of Texas, Arlington, TX 76019, USAColin Kern - Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USAMatthew K Fujita - Department of Biology, University of Texas, Arlington, TX 76019, USAJuan C Opazo - Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, ChileJerzy Jurka - Genetic Information Research Institute, Mountain View, CA 94043, USAKenji K Kojima - Genetic Information Research Institute, Mountain View, CA 94043, USAJuan Caballero - Institute for Systems Biology, Seattle, WA 98109, USARobert M Hubley - Institute for Systems Biology, Seattle, WA 98109, USAArian F Smit - Institute for Systems Biology, Seattle, WA 98109, USARoy N Platt - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USAChristine A Lavoie - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USAMeganathan P Ramakodi - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USAAlexander Suh - Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, SwedenSally R Isberg - Porosus Pty. Ltd., Palmerston, NT 0831, Australia. Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. Centre for Crocodile Research, Noonamah, NT 0837, AustraliaLee Miles - Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, AustraliaAmanda Y Chong - Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, AustraliaWeerachai Jaratlerdsiri - Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, AustraliaJaime Gongora - Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, AustraliaChristopher Moran - Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, AustraliaAndrés Iriarte - Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, UruguayJohn McCormack - Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USAShane C Burgess - College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USAScott V Edwards - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USAEric Lyons - School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USAChristina Williams - Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USAMatthew Breen - Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USAJason T Howard - Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USACathy R Gresham - Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USADaniel G Peterson - Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USAJürgen Schmitz - Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, GermanyDavid D Pollock - Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USADavid Haussler - Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USAEric W Triplett - Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USANaoki Irie - Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, JapanErich D Jarvis - Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USAChristopher A Brochu - Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USACarl J Schmidt - Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USAFiona M McCarthy - School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USABrant C Faircloth - Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90019, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USAFederico G Hoffmann - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USATravis C Glenn - Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USAToni Gabaldón - Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, SpainBenedict Paten - Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USADavid A Ray - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ed@soe.ucsc.edu david.a.ray@ttu.eduGuojie Zhang - University of CopenhagenJohn W Finger Jr - University of Georgia
- Resource Type
- Journal article
- Publication Details
- Science (American Association for the Advancement of Science), Vol.346(6215), 1254449
- DOI
- 10.1126/science.1254449
- PMID
- 25504731
- PMCID
- PMC4386873
- NLM abbreviation
- Science
- ISSN
- 1095-9203
- eISSN
- 1095-9203
- Publisher
- United States
- Grant note
- 1U41HG006992-2 / NHGRI NIH HHS Howard Hughes Medical Institute 5U01HG004695 / NHGRI NIH HHS U41 HG007234 / NHGRI NIH HHS R01 GM097251 / NIGMS NIH HHS R01 HG002939 / NHGRI NIH HHS 1U41HG007234-01 / NHGRI NIH HHS U01 HG004695 / NHGRI NIH HHS U41 HG006992 / NHGRI NIH HHS
- Language
- English
- Date published
- 12/12/2014
- Academic Unit
- Earth and Environmental Sciences; University College Courses
- Record Identifier
- 9983983649002771
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