The Complete Mitochondrial Genome of <i>Squalus cubensis</i> and Comparative Mitogenomics and Phylomitogenomics of the Family Squalidae

The Cuban dogfish, <i>Squalus cubensis</i>, is a benthic shark with a discontinuous distribution in the Western Atlantic Ocean, from North Carolina, USA, to San Matias Gulf, Argentina, and is caught in both commercial and recreational fisheries across its range. <i>Squalus cubensis</i> is listed as "Least Concern" by the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. This study generated the first genomic resource for <i>Squalus cubensis</i>; we assembled and characterized its mitochondrial genome in detail. The AT-rich mitochondrial genome of <i>Squalus cubensis</i> is 16,753 base pairs long and contains 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and one noncoding control region. Preferential usage of the ATT (Ile), TTA (Leu), and CTA (Leu) codons by PCGs contributes to the AT richness of the mitochondrial genome. Selective pressure analysis indicates that all PCGs encoded in the mitochondrial genome are undergoing purifying selection. Similar to other species within the family Squalidae, the Serine 1 tRNA gene exhibited a truncated D-arm, as compared to the typical cloverleaf structure of the other 21 tRNA genes. The 1049-base-pair-long control region contains many AT-rich microsatellite repeats but lacks any tandem repeats. The secondary structure of the control region contains many hairpin loop structures. The completely assembled and analyzed mitochondrial genome of <i>Squalus cubensis</i> will assist biomonitoring programs based on environmental DNA (eDNA) and aid in the accurate identification of specimens belonging to the family Squalidae.