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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C.
Affiliation
  • Green RE; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu.
  • Braun EL; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
  • Armstrong J; 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, USA.
  • Earl D; 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, USA.
  • Nguyen N; 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, USA.
  • Hickey G; 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, USA.
  • Vandewege MW; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
  • St John JA; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
  • Capella-Gutiérrez S; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain.
  • Castoe TA; 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, USA.
  • Kern C; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA.
  • Fujita MK; Department of Biology, University of Texas, Arlington, TX 76019, USA.
  • Opazo JC; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
  • Jurka J; Genetic Information Research Institute, Mountain View, CA 94043, USA.
  • Kojima KK; Genetic Information Research Institute, Mountain View, CA 94043, USA.
  • Caballero J; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Hubley RM; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Smit AF; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Platt RN; 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.
  • Lavoie CA; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
  • Ramakodi MP; 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.
  • Finger JW; Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
  • Suh A; Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden.
  • Isberg SR; 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, Australia.
  • Miles L; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
  • Chong AY; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
  • Jaratlerdsiri W; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
  • Gongora J; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
  • Moran C; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
  • Iriarte A; Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
  • McCormack J; Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA.
  • Burgess SC; College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA.
  • Edwards SV; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Lyons E; School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
  • Williams C; Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.
  • Breen M; Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.
  • Howard JT; Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
  • Gresham CR; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
  • Peterson DG; 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, USA.
  • Schmitz J; Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.
  • Pollock DD; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
  • Haussler D; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA.
  • Triplett EW; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
  • Zhang G; China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
  • Irie N; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.
  • Jarvis ED; Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
  • Brochu CA; Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA.
  • Schmidt CJ; Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA.
  • McCarthy FM; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA.
  • Faircloth BC; 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, USA.
Science ; 346(6215): 1254449, 2014 Dec 12.
Article in En | MEDLINE | ID: mdl-25504731
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Birds / Genome / Evolution, Molecular / Dinosaurs / Alligators and Crocodiles Limits: Animals Language: En Journal: Science Year: 2014 Document type: Article Country of publication: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Birds / Genome / Evolution, Molecular / Dinosaurs / Alligators and Crocodiles Limits: Animals Language: En Journal: Science Year: 2014 Document type: Article Country of publication: United States