DOI: 10.12688/f1000research.73066.3 ISSN: 2046-1402

A Draft Genome Sequence of the Common, or Spectacled Caiman Caiman Crocodilus

Kenichi Okamoto, Nichole Dopkins, Elias Kinfu
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The common, or spectacled, caiman Caiman crocodilus is an abundant, widely distributed Neotropical crocodilian exhibiting notable morphological and molecular diversification. As the type species for the Caimaninae subfamily - the sister taxa for the subfamily to which members of the genus Alligator belong - C . crocodilus occupies a key position in our understanding of crocodilian and archosaur genetics and evolution. The species also accounts by far for the largest share of crocodilian hides on the global market, with the C . crocodilus hide trade alone valued at about US$86.5 million per year. Thus, the genome sequence of C . crocodilus can potentially be of considerable use for both basic and applied research. We obtained 239,911,946 paired-end reads comprising approximately 72 G bases using Illumina™ sequencing of tissue sampled from a single Caiman crocodilus individual. These reads were de-novo assembled and progressively aligned against the genomes of increasingly related crocodilians; liftoff was used to annotate the draft C. crocodilus genome assembly based on an Alligator mississipiensis (a confamilial species) annotation. The draft C. crocodilus genome assembly and sequences reads have been deposited with the National Center for Biotechnology Information with accession numbers JAGPOW000000000.1 for the assembly, and SRR22317059 for the sequence read archives under Bioproject PRJNA716363.

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