Complete Mitochondrial Genome Reveals Little Variation in a Deep-Basin Collection of a Bathypelagic Fish: The Sharpchin Slickhead, Bajacalifornia burragei

The Sharpchin Slickhead, Bajacalifornia burragei, is a rarely collected bathypelagic fish endemic to the eastern tropical Pacific Ocean, and its genetic diversity remains undocumented. This study characterizes mitochondrial diversity in a localized deep-basin collection from the Carmen Basin of the Gulf of California by sequencing complete mitochondrial genomes from four individuals collected simultaneously at 1300 m in a single Tucker trawl. A high-quality reference mitogenome was assembled using PacBio HiFi long reads, and three additional mitogenomes were generated from Illumina PE150 libraries mapped to this reference. The mitogenome of B. burragei exhibits the canonical 37 gene architecture and conserved gene order typical of teleost mitogenomes. Overall mitogenome divergence was low (Range: 0.21–0.29%), with most protein-coding and rRNA genes exceeding 99.5% identity. Slightly elevated variation occurred in atp8, nad6, and several tRNA genes. This study provides the first genetic characterization of B. burragei and establishes a baseline for evaluating mitochondrial diversity within a localized collection of individuals and provides a point of comparison for future studies assessing connectivity among deep basins.