Publication Date:
2014-12-17
Description:
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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Richard E -- Braun, Edward L -- Armstrong, Joel -- Earl, Dent -- Nguyen, Ngan -- Hickey, Glenn -- Vandewege, Michael W -- St John, John A -- Capella-Gutierrez, 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 Jr -- Suh, Alexander -- Isberg, Sally R -- Miles, Lee -- Chong, Amanda Y -- Jaratlerdsiri, Weerachai -- Gongora, Jaime -- Moran, Christopher -- Iriarte, Andres -- McCormack, John -- Burgess, Shane C -- Edwards, Scott V -- Lyons, Eric -- Williams, Christina -- Breen, Matthew -- Howard, Jason T -- Gresham, Cathy R -- Peterson, Daniel G -- Schmitz, Jurgen -- 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 -- Hoffmann, Federico G -- Glenn, Travis C -- Gabaldon, Toni -- Paten, Benedict -- Ray, David A -- 1U41HG006992-2/HG/NHGRI NIH HHS/ -- 1U41HG007234-01/HG/NHGRI NIH HHS/ -- 5U01HG004695/HG/NHGRI NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- U41 HG006992/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; 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. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. ; 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. ; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA. ; Department of Biology, University of Texas, Arlington, TX 76019, USA. ; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. ; Genetic Information Research Institute, Mountain View, CA 94043, USA. ; Institute for Systems Biology, Seattle, WA 98109, USA. ; 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 Environmental Health Science, University of Georgia, Athens, GA 30602, USA. ; Institute of Experimental Pathology (ZMBE), University of Munster, D-48149 Munster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden. ; 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. ; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. ; Departamento de Desarrollo Biotecnologico, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo, Uruguay. ; Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA. ; College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. ; School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA. ; Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; 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. ; Institute of Experimental Pathology (ZMBE), University of Munster, D-48149 Munster, Germany. ; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. ; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA. ; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. ; China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. ; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan. ; Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA. ; Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA. ; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA. ; 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. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain. ; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. ; 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.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504731" target="_blank"〉PubMed〈/a〉
Keywords:
Alligators and Crocodiles/classification/*genetics
;
Animals
;
Biological Evolution
;
Birds/classification/*genetics
;
Conserved Sequence
;
DNA Transposable Elements
;
Dinosaurs/classification/*genetics
;
*Evolution, Molecular
;
Genetic Variation
;
*Genome
;
Molecular Sequence Annotation
;
Molecular Sequence Data
;
Phylogeny
;
Reptiles/classification/genetics
;
Sequence Alignment
;
Sequence Analysis, DNA
;
Transcriptome
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
Permalink
