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2. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Author

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, Hoffmann, Federico G, Glenn, Travis C, Gabaldón, Toni, Paten, Benedict, and Ray, David A

Subjects
Genetics, Human Genome, Alligators and Crocodiles, Animals, Biological Evolution, Birds, Conserved Sequence, DNA Transposable Elements, Dinosaurs, Evolution, Molecular, Genetic Variation, Genome, Molecular Sequence Annotation, Molecular Sequence Data, Phylogeny, Reptiles, Sequence Alignment, Sequence Analysis, DNA, Transcriptome, General Science & Technology
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.

Published
2014

4. Nucleic Acid Preservation Card Surveillance Is Effective for Monitoring Arbovirus Transmission on Crocodile Farms and Provides a One Health Benefit to Northern Australia

Author

Kurucz, Nina, primary, McMahon, Jamie Lee, additional, Warchot, Allan, additional, Hewitson, Glen, additional, Barcelon, Jean, additional, Moore, Frederick, additional, Moran, Jasmin, additional, Harrison, Jessica J., additional, Colmant, Agathe M. G., additional, Staunton, Kyran M., additional, Ritchie, Scott A., additional, Townsend, Michael, additional, Steiger, Dagmar Meyer, additional, Hall, Roy A., additional, Isberg, Sally R., additional, and Hall-Mendelin, Sonja, additional

Published
2022
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8. Mosquito-Independent Transmission of West Nile virus in Farmed Saltwater Crocodiles (Crocodylus porosus)

Author

Habarugira, Gervais, primary, Moran, Jasmin, additional, Colmant, Agathe M.G., additional, Davis, Steven S., additional, O’Brien, Caitlin A., additional, Hall-Mendelin, Sonja, additional, McMahon, Jamie, additional, Hewitson, Glen, additional, Nair, Neelima, additional, Barcelon, Jean, additional, Suen, Willy W., additional, Melville, Lorna, additional, Hobson-Peters, Jody, additional, Hall, Roy A., additional, Isberg, Sally R., additional, and Bielefeldt-Ohmann, Helle, additional

Published
2020
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10. A genetic linkage map for the saltwater crocodile (Crocodylus porosus)

Author

Lance Stacey L, Glenn Travis C, Isberg Sally R, Miles Lee G, Dalzell Pauline, Thomson Peter C, and Moran Chris

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1). Conclusion We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers placed on this genetic map have been evaluated in up to 18 other extant species of crocodilian, this map will be of intrinsic value to comparative mapping efforts aimed at understanding genome content and organization among crocodilians, as well as the molecular evolution of reptilian and other amniote genomes. As researchers continue to work towards elucidation of the crocodilian genome, this first generation map lays the groundwork for more detailed mapping investigations, as well as providing a valuable scaffold for future genome sequence assembly.

Published
2009
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12. Diagnostic investigation of new disease syndromes in farmed Australian saltwater crocodiles (Crocodylus porosus) reveals associations with herpesviral infection

Author

Shilton, Catherine M., primary, Jerrett, Ian V., additional, Davis, Steven, additional, Walsh, Susan, additional, Benedict, Suresh, additional, Isberg, Sally R., additional, Webb, Grahame J. W., additional, Manolis, Charlie, additional, Hyndman, Timothy H., additional, Phalen, David, additional, Brown, Gregory P., additional, and Melville, Lorna, additional

Published
2016
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13. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Author

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., 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, Juergen, 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., 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., 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, Juergen, 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, and Ray, David A.

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.

Published
2014
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14. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC

Author

Jaratlerdsiri, Weerachai, Deakin, Janine, Godinez, Ricardo M., Shan, Xueyan, Peterson, Daniel G., Marthey, Sylvain, Lyons, Eric, McCarthy, Fiona M., Isberg, Sally R., Higgins, Damien P., Chong, Amanda Y., John, John St, Glenn, Travis C., Ray, David A., Gongora, Jaime, Jaratlerdsiri, Weerachai, Deakin, Janine, Godinez, Ricardo M., Shan, Xueyan, Peterson, Daniel G., Marthey, Sylvain, Lyons, Eric, McCarthy, Fiona M., Isberg, Sally R., Higgins, Damien P., Chong, Amanda Y., John, John St, Glenn, Travis C., Ray, David A., and Gongora, Jaime

Abstract

The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

Published
2014

15. Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC

Author

Jaratlerdsiri, Weerachai, primary, Deakin, Janine, additional, Godinez, Ricardo M., additional, Shan, Xueyan, additional, Peterson, Daniel G., additional, Marthey, Sylvain, additional, Lyons, Eric, additional, McCarthy, Fiona M., additional, Isberg, Sally R., additional, Higgins, Damien P., additional, Chong, Amanda Y., additional, John, John St, additional, Glenn, Travis C., additional, Ray, David A., additional, and Gongora, Jaime, additional

Published
2014
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18. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

Author

St John, John A, primary, Braun, Edward L, additional, Isberg, Sally R, additional, Miles, Lee G, additional, Chong, Amanda Y, additional, Gongora, Jaime, additional, Dalzell, Pauline, additional, Moran, Christopher, additional, Bed'Hom, Bertrand, additional, Abzhanov, Arkhat, additional, Burgess, Shane C, additional, Cooksey, Amanda M, additional, Castoe, Todd A, additional, Crawford, Nicholas G, additional, Densmore, Llewellyn D, additional, Drew, Jennifer C, additional, Edwards, Scott V, additional, Faircloth, Brant C, additional, Fujita, Matthew K, additional, Greenwold, Matthew J, additional, Hoffmann, Federico G, additional, Howard, Jonathan M, additional, Iguchi, Taisen, additional, Janes, Daniel E, additional, Khan, Shahid Yar, additional, Kohno, Satomi, additional, de Koning, AP Jason, additional, Lance, Stacey L, additional, McCarthy, Fiona M, additional, McCormack, John E, additional, Merchant, Mark E, additional, Peterson, Daniel G, additional, Pollock, David D, additional, Pourmand, Nader, additional, Raney, Brian J, additional, Roessler, Kyria A, additional, Sanford, Jeremy R, additional, Sawyer, Roger H, additional, Schmidt, Carl J, additional, Triplett, Eric W, additional, Tuberville, Tracey D, additional, Venegas-Anaya, Miryam, additional, Howard, Jason T, additional, Jarvis, Erich D, additional, Guillette, Louis J, additional, Glenn, Travis C, additional, Green, Richard E, additional, and Ray, David A, additional

Published
2012
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19. Distribution of Endogenous Retroviruses in Crocodilians

Author

Jaratlerdsiri, Weerachai, primary, Rodríguez-Zárate, Clara J., additional, Isberg, Sally R., additional, Damayanti, Chandramaya Siska, additional, Miles, Lee G., additional, Chansue, Nantarika, additional, Moran, Chris, additional, Melville, Lorna, additional, and Gongora, Jaime, additional

Published
2009
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21. Sequencing Three Crocodilian Genomes to Illuminate the Evolution of Archosaurs and Amniotes

Author

St John, John A, Braun, Edward L, Isberg, Sally R, Miles, Lee G, Chong, Amanda Y, Gongora, Jaime, Dalzell, Pauline, Bed'Hom, Bertrand, Burgess, Shane C, Cooksey, Amanda M, Castoe, Todd A, Densmore, Llewellyn D, Drew, Jennifer C, Faircloth, Brant C, Greenwold, Matthew J, Hoffmann, Federico G, Howard, Jonathan M, Iguchi, Taisen, Janes, Daniel E, Khan, Shahid Yar, Kohno, Satomi, de Koning, AP Jason, Lance, Stacey L, McCarthy, Fiona M, McCormack, John E, Merchant, Mark E, Peterson, Daniel G, Pollock, David D, Pourmand, Nader, Raney, Brian J, Roessler, Kyria A, Sanford, Jeremy R, Sawyer, Roger H, Schmidt, Carl J, Triplett, Eric W, Tuberville, Tracey D, Venegas-Anaya, Miryam, Howard, Jason T, Jarvis, Erich D, Guillette, Louis J, Glenn, Travis C, Ray, David A, Moran, Christopher J, Abzhanov, Arkhat, Crawford, Nicholas G., Moran, Christopher, Edwards, Scott V., Fujita, Matthew, and Green, Richard E.

Subjects
genomics, evolution, Crocodylia, Archosauria, amniote
Abstract

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described., Organismic and Evolutionary Biology

Published
2012
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