Genome sequencing
Ghosh, A., Johnson, M.G., Osmanski, A.B., Louha, S. Bayona-Vásquez, N.J., Glenn, T.C., Gongora, J., Green, R.E., Isberg, S., Stevens, R.D., Ray D.A. (2020) A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae. Genome Biology and Evolution 12(1): 3635-3646.
Ghosh, A. Platt, R.N., Vandewege, M.W., Tabassum, R., Hsu, C-Y, Isberg, S.R., Peterson, D.G., Finger, J.W., Kieran, T.J., Glenn, T.C., Gongora, J., Ray D.A. (2020) Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus.Analytical Biochemistry 113781, doi:10.1016/j.ab.2020.113781.
Green, R.E., Braun, E.L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M.W., St John, J.A., Capella-Gutiérrez, S., Castoe, T.A., Kern, C., Fujita, M.K., Opazo, J.C., Jurka, J., Kojima, K.K., Caballero, J., Hubley, R.M., Smit, A.F., Platt, R.N., Lavoie, C.A., Ramakodi, M.P., Finger, Jr. J.W., Suh, A., Isberg, S.R., Miles, L., Chong, A.Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S.C., Edwards, S.V., Lyons, E., Williams, C., Breen, M., Howard, J.T., Gresham, C.R., Peterson, D.G., Schmitz, J., Pollock, D.D., Haussler, D., Triplett, E.W., Zhang, G., Irie, N., Jarvis, E.D., Brochu, C.A., Schmidt, C.J., McCarthy, F.M., Faircloth, B.C., Hoffmann, F.G., Glenn, T.C., Gabaldón, T., Paten, B., Ray, D.A. (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.Science 346: 1254449.
St John, J.A., Braun, E.L., Isberg, S.R., Miles, L.G., Chong, A.Y., Gongora, J., Dalzell, P., Moran, C., Bedhom, B., Abzhanov, A., Burgess, S.C., Cooksey, A.M., Castoe, T.A., Crawford, N.G., Densmore, L.D., Drew, J.C., Edwards, S.V., Faircloth, B.C., Fujita, M.K., Greenwold, M.J., Hoffmann, F.G., Howard, J.M., Iguchi, T., Janes, D.E., Khan, S.Y., Kohno, S., de Koning, A.J., Lance, S.L., McCarthy, F.M., McCormack, J.E., Merchant, M.E., Peterson, D.G., Pollock, D.D., Pourmand, N., Raney, B.J., Roessler K.A., Sanford, J.R., Sawyer, R.H., Schmidt, C.J., Triplett, E.W., Tuberville, T.D., Venegas-Anaya, M., Howard, J.T., Jarvis, E.D., Guillette, L.J-Jr., Glenn, T.C., Green, R.E., Ray, D.A. (2012). Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.Genome Biology. 13:415.
Dalzell, P, Miles, L.G., Isberg, S.R., Glenn, T.C., King, C., Murtagh, V., Moran, C. (2010) Standardised reference ideogram for physical mapping in the saltwater crocodile (Crocodylus porosus). Cytogenetics and Genomics 127:204-212.
Miles, L.G., Isberg, S.R., Glenn, T.C., Lance, S.L., Dalzell, P., Thomson, P.C., Moran, C. (2009) A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics 10:339.
Isberg, S., Johnston, S., Chen, Y., Barker, S., Moran, C. (2006) First evidence of higher female recombination in a species with temperature-dependant sex determination: the saltwater crocodile. Journal of Heredity 97(6): 599-602.
Endogenous retroviruses
Chong, A.Y., Korma, K.K., Jurka, J., Ray, D.A., Smit, A.F.A., Isberg, S.R., Gongora, J. (2014) Evolution and gene capture in ancient endogenous retroviruses – insights from the crocodilian genomes. Retrovirology 11:71.
Chong, A.Y., Atkinson, S.J,. Isberg, S., Gongora, J. (2012) Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia. Mobile DNA 3:20.
Immunogenetics
Milic, N.L., Davis, S., Carr, J.M., Isberg, S., Beard, M.R., Helbig, K.J. (2015) Sequence analysis and characterization of virally induced viperin in the saltwater crocodile. Developmental and Comparative Immunology 51: 108-115.
Jaratlerdsiri, W., Deakin, J., Godinez, R.M., Shan, X., Peterson, D.G., Marthey, S., Lyons, E., McCarthy, F.M., Isberg, S.R., Higgins, D.P., Chong, A.Y., St John, J., Glenn, T.C., Ray, D.A., Gongora, J. (2014) Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PloS ONE 9(12):e114631.
Jaratlerdsiri, W., Isberg, S.R., Higgins, D.P., Ho, S.Y.W., Salomonsen, J., Skjodt, K., Miles, L.G., Gongora, J. (2014). Evolution of MHC class I in the Order Crocodylia. Immunogenetics 66: 53-65.
Jaratlerdsiri, W., Isberg, S., Higgins, D., Miles, L., Gongora, J. (2014). Selection and Trans-Species Polymorphism of Major Histocompatibility Complex Class II Genes in the Order Crocodylia. PLOS ONE 9(2), 1-13.
Jaratlerdsiri, W., Isberg, S., Higgins, D., Gongora, J. (2012). MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection.Immunogenetics 64: 825-838.
Jaratlerdsiri, W., Rodriguez-Zarate, C.J., Isberg, S.R., Damayanti, C.S., Miles, L.G., Chansue, N., Moran, C., Melville, L., Gongora, J. (2009) Distribution of endogenous retroviruses in crocodilians.Journal of Virology 83: 10305-10308, doi10.1128/JVI.00668-09.
