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2. Application of chimeric antigens to paper-based diagnostics for detection of West Nile virus infections ofCrocodylus porosus –a novel animal test case

Author

Johnston, Ryan A., primary, Habarugira, Gervais, additional, Harrison, Jessica J., additional, Isberg, Sally R., additional, Moran, Jasmin, additional, Morgan, Mahali, additional, Davis, Steven S., additional, Melville, Lorna, additional, Howard, Christopher B., additional, Henry, Charles S., additional, Macdonald, Joanne, additional, Bielefeldt-Ohmann, Helle, additional, Hall, Roy A., additional, and Hobson-Peters, Jody, additional

Published
2024
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4. 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

9. 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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13. AVIAN GENOMICS: 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., Jr., 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.

Published
2014
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19. Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus

Author

Ghosh, Arnab, primary, Platt, Roy N., additional, Vandewege, Michael W., additional, Tabassum, Rabia, additional, Hsu, Chuan-Yu, additional, Isberg, Sally R., additional, Peterson, Daniel G., additional, Finger, John W., additional, Kieran, Troy J., additional, Glenn, Travis C., additional, Gongora, Jaime, additional, and Ray, David A., additional

Published
2020
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20. 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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24. 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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27. 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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30. 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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32. Simulating economic values of a genetic improvement program for Australian farmed saltwater crocodiles

Author

Gray, Emily M., Ahmadi-Esfahani, Fredoun Z., and Isberg, Sally R.

Subjects
Resource /Energy Economics and Policy
Abstract

In genetic improvement programs, candidates for breeders are ranked by the profitability of their offspring, expressed as a weighted sum of the genetic gain from selection. In this paper, we estimate the economic values of a genetic improvement program for Australian farmed saltwater crocodiles. A bioeconomic profit function for a representative breeding pair is used to determine the optimal slaughter age following genetic improvement in each selection objective. The results indicate that estimated farm profitability increases by nearly # A111 for a 1-week reduction in juvenile slaughter age, # A78 for a 1 per cent increase in the proportion of first-grade skins produced, and # A33 for an increase in the number of viable hatchlings per clutch. The implications of the analysis for the Australian crocodile industry and the limitations of the research are explored.

Published
2007
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34. Evolution of MHC class I in the Order Crocodylia

Author

Jaratlerdsiri, Weerachai, primary, Isberg, Sally R., additional, Higgins, Damien P., additional, Ho, Simon Y. W., additional, Salomonsen, Jan, additional, Skjodt, Karsten, additional, Miles, Lee G., additional, and Gongora, Jaime, additional

Published
2013
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36. 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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37. Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia

Author

Luck, Naomi L., primary, Thomas, Kristen C., additional, Morin-Adeline, Victoria E., additional, Barwick, Sophie, additional, Chong, Amanda Y., additional, Carpenter, Eliza L., additional, Wan, LinXiao, additional, Willet, Cali E., additional, Langford-Salisbury, Shannan M., additional, Abdelsayd, Mary, additional, Ang, Rachel A., additional, Atkinson, Sarah J., additional, Barcelo, Fabian G., additional, Booth, Melanie E., additional, Bradbury, Emma J., additional, Branighan, Thomas L., additional, Brown, Jennifer, additional, Castillo, Lesley E., additional, Chandler, Nichola D., additional, Chong, Josephine Y., additional, Collits, Kimberly J., additional, Cook, Emma, additional, Cruz, Rachel E., additional, Farrugia, Claire A., additional, Fletcher, Jessica L., additional, Fletcher, Sophie, additional, Gamaliel, Nicole S., additional, Gurr, Jessica F., additional, Hallett, Nathan J., additional, Hargreaves, Grace, additional, Harris, Teresa, additional, Hollings, Samantha, additional, Hopcroft, Ryan L., additional, Johinke, Danielle, additional, Kern, Pippa L., additional, Kiddell, Jane L., additional, Kilby, Kristen E., additional, Kragic, Borjana, additional, Kwan, Jacqueline H., additional, Lee, Joseph I., additional, Liang, Jennifer M., additional, Lillie, Mette C., additional, Lui, Belle C., additional, Luk, Sharon W., additional, Lun, Kwok H., additional, Marshall, Kate L., additional, Marzec, Jolanta A., additional, Masters, Kellie T., additional, Mazurkijevic, Laura J., additional, Medlock, Jeremy, additional, Meoli, Christopher, additional, Morris, Katrina M., additional, Noh, Yvonne H., additional, Okazaki, Hana, additional, Orourke, Tamara J., additional, Payne, Elyssa M., additional, Powell, Dean J., additional, Quinlivan, Antonia R., additional, Reeves, Thomas J., additional, Robson, Kate, additional, Robson, Kate L., additional, Royle, Leah J., additional, Stevenson, Ryan, additional, Sellens, Teigan, additional, Sun, ZiChen, additional, Sutton, Amanda L., additional, Swan, Amelia, additional, Tang, Jason M., additional, Tinker, Jarrod E., additional, Tomlinson, Suzanne C., additional, Wilkin, Tessa, additional, Wright, Amanda L., additional, Xiao, Sam T., additional, Yang, Jessica, additional, Yee, Christine, additional, Jaratlerdsiri, Weerachai, additional, Isberg, Sally R., additional, Miles, Lee, additional, Higgins, Damien, additional, Lane, Amanda, additional, and Gongora, Jaime, additional

Published
2012
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38. 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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43. 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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44. Unexpected lower testosterone in faster growing farmed saltwater crocodile (Crocodylus porosus) hatchlings.

Author

Jr.Finger, John W., Thomson, Peter C., and Isberg, Sally R.

Subjects
*TESTOSTERONE, *CROCODYLUS porosus, *AGRICULTURAL productivity, *CORTICOSTERONE, *SEX hormones
Abstract

Agricultural production of the saltwater crocodile ( Crocodylus porosus ) is an emergent industry in northern Australia with many of the factors affecting production remaining unknown. In this study, we sought to expand upon our previous findings of reference corticosterone and immune function by reporting baseline sex hormone levels [testosterone (TEST) and estradiol (ESTR)] and their association with growth. This was achieved by sampling 253 hatchling crocodiles repeatedly at 3, 6, and 9 months of age. Sampling age had a significant effect on both TEST ( p < 0.001) and ESTR ( p < 0.001) suggesting climatic/abiotic factors have an influence even in prepubescent crocodiles. Stress, as measured by plasma corticosterone, had no detectable effect on plasma ESTR or TEST levels. Unexpectedly however, TEST was higher in slower-growing crocodiles, which is contrary to what has been reported for the American alligator. ESTR was not associated with growth. [ABSTRACT FROM AUTHOR]

Published
2016
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45. Reference levels for corticosterone and immune function in farmed saltwater crocodiles (Crocodylus porosus) hatchlings using current Code of Practice guidelines.

Author

Jr.Finger, John W., Thomson, Peter C., Adams, Amanda L., Benedict, Suresh, Moran, Christopher, and Isberg, Sally R.

Subjects
*CORTICOSTERONE, *CROCODYLUS porosus, *CROCODILES, *IMMUNE response, *GROWTH rate, *ESCHERICHIA coli
Abstract

To determine reference levels for on-farm stressors on immune responsiveness and growth rate, 253 hatchling crocodiles from 11 known breeding pairs were repeatedly measured and blood sampled during their first year. Plasma corticosterone (CORT) was used to quantify baseline stress levels in captive animals and were found to be lower (mean 1.83 ± SE 0.16 ng/mL) than previously reported in saltwater crocodile hatchlings. Two tests of immune function were also conducted. Innate constitutive immunity was assessed using bacterial killing assays (BKA) against two bacterial species: Escherichia coli and Providencia rettgeri , whereby the latter causes considerable economic loss to industry from septicaemic mortalities. Although the bactericidal capabilities were different at approximately 4 months old (32 ± 3% for E. coli and 16 ± 4% for P. rettgeri ), the differences had disappeared by approximately 9 months old (58 ± 2% and 68 ± 6%, respectively). To assess immune responsiveness to a novel antigen, the inflammatory swelling response caused by phytohaemagglutinin (PHA) injection was assessed but was only significantly different between Samplings 1 and 3 (5% LSD). There were no significant clutch effects for CORT or PHA but there were for both BKA traits. CORT was not significantly associated with growth (head length) or the immune parameters except for P. rettgeri BKA where higher CORT levels were associated with better bactericidal capability. As such, these results suggest that the crocodiles in this study are not stressed, therefore endorsing the management strategies adopted within the Australian industry Code of Practice. [ABSTRACT FROM AUTHOR]

Published
2015
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