A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae

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dc.creatorGhosh, Arnab (TTU)
dc.creatorJohnson, Matthew G. (TTU)
dc.creatorOsmanski, Austin B. (TTU)
dc.creatorLouha, Swarnali
dc.creatorBayona-Vásquez, Natalia J.
dc.creatorGlenn, Travis C.
dc.creatorGongora, Jaime
dc.creatorGreen, Richard E.
dc.creatorIsberg, Sally
dc.creatorStevens, Richard D. (TTU)
dc.creatorRay, David A. (TTU)
dc.date.accessioned2023-05-01T15:02:55Z
dc.date.available2023-05-01T15:02:55Z
dc.date.issued2019
dc.description© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. cc-by
dc.description.abstractCrocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C. porosus and 6 in Alligator mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.
dc.identifier.citationGhosh, A., Johnson, M.G., Osmanski, A.B., Louha, S., Bayona-Vasquez, N.J., Glenn, T.C., Gongora, J., Green, R.E., Isberg, S., Stevens, R.D., & Ray, D.A.. 2019. A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae. Genome Biology and Evolution, 12(1). https://doi.org/10.1093/gbe/evz269
dc.identifier.urihttps://doi.org/10.1093/gbe/evz269
dc.identifier.urihttps://hdl.handle.net/2346/93059
dc.language.isoeng
dc.subjectCrocodylus porosus
dc.subjectevolution
dc.subjectselection
dc.titleA High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae
dc.typeArticle

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