Target-capture sequencing (TCS) is typically designed to recover nuclear genes, yet it also produces “off-target” DNA reads that represent a valuable resource for recovering mitochondrial data. Despite being one of the most ecologically diverse and speciose reef-fish families, Labridae (wrasses and parrotfishes) remains underrepresented in mitochondrial genetic data. In this study, we leveraged off-target reads from a published ultraconserved element (UCE) dataset to assemble complete mitochondrial genomes for 68 species of wrasses and parrotfishes, 54 of which were novel to public genetic repositories. Overall, the novel genetic data produced in this study more than doubled the number of complete mitogenomes for the family Labridae on reference sequence databases.
Using this data, we reconstructed the most comprehensive mitochondrial phylogeny for labrids to date, recovering all eight recognised subfamilies with strong support. Comparison with published UCE-based nuclear phylogenies identified differences in the placement of subfamily Cirrhilabrinae. The novel mitogenomic data generated in this study provide a valuable foundation for future investigations into evolutionary processes, such as interspecific hybridisation and incomplete lineage sorting, that may help disentangle the complex evolutionary relationships within Labridae. Finally, our findings highlight the benefit of mining off-target TCS reads to rapidly expand organellar genetic resources, providing complementary mitochondrial data to investigate evolutionary dynamics in marine taxa.