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To improve researchers\u2019 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\u2009Mb, with N50 scaffold size of 17.7\u2009Mb and N90 scaffold size of 3.8\u2009Mb. 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.\u00a0porosus and 6 in Alligator mississippiensis. The annotated C.\u00a0porosus 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.<\/jats:p>","DOI":"10.1093\/gbe\/evz269","type":"journal-article","created":{"date-parts":[[2019,12,7]],"date-time":"2019-12-07T23:13:57Z","timestamp":1575760437000},"page":"3635-3646","source":"Crossref","is-referenced-by-count":21,"title":["A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae"],"prefix":"10.1093","volume":"12","author":[{"given":"Arnab","family":"Ghosh","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Texas Tech University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew G","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, 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