Mining for mitochondria: 68 mitogenomes for wrasses and parrotfishes (F: Labridae) from off-target UCE data

Labridae (wrasses and parrotfishes) is one of the most ecologically diverse families of reef-associated fishes but remains underrepresented in mitochondrial genomic resources. The availability of complete mitochondrial genomes is critical for both evolutionary and ecological research, since they are increasingly being used across population genetic, phylogenetic, species identification and eDNA studies. A low-cost method to increase mitogenomic representation is to leverage off-target reads produced in target-capture sequencing (TCS). Here we use a recently published ultraconserved elements (UCE) dataset for Labridae to assemble and annotate off-target reads to produce complete mitogenomes for 68 species within Labridae, 54 of which are novel to NCBI. These novel complete mitogenomes expand the taxonomic coverage of labrid mitogenomes from less than 5% and 12% to 13% and 20% on NCBI’s RefSeq and Nucleotide databases. We also recovered partial mitogenomes for a further 191 species in the family. Comparative analyses revealed that the lengths of the mitogenomes varied between 16,320 and 17,288 bp. While protein-coding genes (PCGs), rRNAs and tRNAs exhibited little variation, the D-loop showed notable length variability, consistent with trends observed in other fish lineages. Comparisons among labrid tribes highlighted Cirrhilabrinae as having the longest mitogenomes (average=17.2 kbp), while Julidinae displayed the broadest size range (16.3-17.1 kbp), likely due to its higher species richness and representation in the original UCE dataset. Phylogenetic reconstruction using all 13 PCGs and two rRNAs confirmed the eight-tribe topology previously seen within Labridae, each with strong nodal support. Although some topological discordance was observed when compared to previously published labrid phylogenies (e.g. the placement of tribe Cirrhilabrinae) systematic relations are relatively consistent with previous phylogenies of the family. These results significantly expand the mitogenomic representation within Labridae, providing a valuable resource for future phylogenetic and evolutionary studies in this family of reef fish. It also highlights the additional value that can be gained from off-target reads of TCS data.