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Complete mitochondrial genome of the Caribbean reef shark, Carcharhinus perezi (Carcharhinformes: Carcharhinidae)

Citation

Gallagher, Austin (2021), Complete mitochondrial genome of the Caribbean reef shark, Carcharhinus perezi (Carcharhinformes: Carcharhinidae), Dryad, Dataset, https://doi.org/10.5061/dryad.qjq2bvqfh

Abstract

The Caribbean reef shark Carcharhinus perezi is a medium to large-bodied coastal and reef-associated predator found throughout the subtropical and tropical waters of the Atlantic Ocean and Caribbean Sea, although its populations are increasingly threatened by overfishing. We describe the first mitochondrial genome sequence for this species, using Illumina MiSeq sequencing of an individual from The Bahamas. We report the mitogenome sequence of the Caribbean reef shark to be 16,709 bp and composed two rRNA genes, 22 tRNA genes, 13 protein-coding genes, two non-coding genes; the control region and the origin of light-strand replication. We discuss the implications of this new information on future monitoring efforts and conservation measures such as marine protected areas, and urge future mitochondrial studies of sharks to expand their reach into the Atlantic Ocean.

Methods

Mitochondrial DNA genome sequence data for Caribbean reef shark C. perezi. 

We describe the complete mitochondrial genome of the Caribbean reef shark. A 2 mm muscle sample was taken from a live, mature female individual (177 cm total length, identification tag: 39093) sampled from the waters off Great Exumas, The Commonwealth of The Bahamas (23.726984 N, -76.033982 W) on February 20, 2019 (the shark was released alive). The sample was immediately frozen, and later transported to the Center for Genome Innovation (CGI) at the University of Connecticut (USA) for genomic DNA extraction.

Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following manufacturer protocol.  Genomic DNA (deposited and stored at the CGI) was quantified, purity ratios determined using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).  To further assess DNA quality, genomic DNA was analyzed on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) using the Genomic DNA assay.  Whole genome shotgun libraries were made using the Illumina Nextera XT library preparation kit following manufacturer protocol (Illumina, San Diego, CA).  Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies, Santa Clara, CA, USA) then quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Life Technologies, Carlsbad, CA, USA).  Libraries were prepared for sequencing on the Illumina MiSeq using version 2 chemistry for paired end 250bp reads.