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 ORCID: https://orcid.org/0000-0002-8979-9992, 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., Hoffmann, Federico G., Glenn, Travis C., Gabaldón, Toni, Paten, Benedict and Ray, David A. (2014) Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346 (6215). ISSN 0036-8075

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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.

Item Type: Article
Additional Information: Funding Information: Genome drafts have been submitted to the National Center for Biotechnology Information repository under the following accession numbers: Alligator mississippiensis, AKHW00000000; Crocodylus porosus, JRXG00000000; Gavialis gangeticus, JRWT00000000. Supplemental files have been archived at GigaScience (DOIs: 10.5524/100125, 10.5524/100126, 10.5524/100127, and 10.5524/100128) and at crocgenomes.org. This project was conducted by the International Crocodilian Genomes Working Group (ICGWG; www.crocgenomes.org). Supported by NSF grants MCB-1052500 and DEB-1020865 (D.A.R.), MCB-0841821 (D.A.R., D.G.P., F.M.M., C.J.S.), DUE-0920151 (E.L.B., E.W.T.), DBI-0905714 (M.K.F.), and DEB-1242260 (B.C.F.). D.A.R., F.M.M., and D.G.P. were also supported by the Institute for Genomics, Biocomputing and Biotechnology at Mississippi State University. S.R.I., L.G.M., J.G., and CM. were supported by Australian Rural Industries Research and Development Corporation grants (RIRDC PRJ-000549, RIRDC PRJ-005355, RIRDC PRJ-002461). R.E.G. is a Searle Scholar, Sloan Fellow, and consultant for Dovetail Genomics. E.D.J. was supported by the Howard Hughes Medical Institute and the National Institutes of Health. E.L. received support from the Gordon and Betty Moore Foundation (#3383). R. Elsey, S. Lance, and T. Tuberville aided in collecting alligator samples. The following centers were vital in permitting the computational analyses required for this project: The High Performance Computing Collaborative (HPC2) at Mississippi State University, the High Performance Computing Center at Texas Tech University, the Georgia Advanced Computing Resource Center at the University of Georgia, the University of Florida High Performance Computing Center. The National Institutes of Health provided funding for UCSC infrastructure used in computing whole genome alignments and ancestral genome reconstructions (1U41HG007234-01, 1U41HG006992-2, 5U01HG004695). Finally, we are grateful to K. Vliet and D. Barber for providing access to fresh gharial blood. Funding Information: Genome drafts have been submitted to the National Center for Biotechnology Information repository under the following accession numbers: Alligator mississippiensis, AKHW00000000; Crocodylus porosus, JRXG00000000; Gavialis gangeticus, JRWT00000000. Supplemental files have been archived at GigaScience (DOIs: 10.5524/100125, 10.5524/100126, 10.5524/100127, and 10.5524/ 100128) and at crocgenomes.org. This project was conducted by the International Crocodilian Genomes Working Group (ICGWG; www.crocgenomes.org). Supported by NSF grants MCB-1052500 and DEB-1020865 (D.A.R.), MCB-0841821 (D.A.R., D.G.P., F.M.M., C.J.S.), DUE-0920151 (E.L.B., E.W.T.), DBI-0905714 (M.K.F.), and DEB-1242260 (B.C.F.). D.A.R., F.M.M., and D.G.P. were also supported by the Institute for Genomics, Biocomputing and Biotechnology at Mississippi State University. S.R.I., L.G.M., J.G., and C.M. were supported by Australian Rural Industries Research and Development Corporation grants (RIRDC PRJ-000549, RIRDC PRJ-005355, RIRDC PRJ-002461). R.E.G. is a Searle Scholar, Sloan Fellow, and consultant for Dovetail Genomics.. E.D.J. was supported by the Howard Hughes Medical Institute and the National Institutes of Health. E.L. received support from the Gordon and Betty Moore Foundation (#3383). R. Elsey, S. Lance, and T. Tuberville aided in collecting alligator samples. The following centers were vital in permitting the computational analyses required for this project: The High Performance Computing Collaborative (HPC2) at Mississippi State University, the High Performance Computing Center at Texas Tech University, the Georgia Advanced Computing Resource Center at the University of Georgia, the University of Florida High Performance Computing Center. The National Institutes of Health provided funding for UCSC infrastructure used in computing whole genome alignments and ancestral genome reconstructions (1U41HG007234-01, 1U41HG006992-2, 5U01HG004695). Finally, we are grateful to K. Vliet and D. Barber for providing access to fresh gharial blood.
Uncontrolled Keywords: general ,/dk/atira/pure/subjectarea/asjc/1000
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 16 Sep 2022 15:36
Last Modified: 23 Sep 2022 16:33
URI: https://ueaeprints.uea.ac.uk/id/eprint/88420
DOI: 10.1126/science.1254449

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