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 almost 13% and 20% on NCBI's RefSeq and Nucleotide databases, respectively. Partial mitochondrial genes were also recovered for 191 additional species in the family. Mitogenome lengths ranged from 16,320 to 17,288 bp with highly conserved protein-coding genes, rRNAs and tRNAs. The non-coding D-loop region showed the most length variation, ranging from 626 to 1556 bp. Species from the Cirrhilabrinae tribe had the longest mitogenomes (average = 17.2 kbp), while species from the Julidinae tribe displayed the broadest size range (16.3-17.1 kbp), likely due to their higher species richness and representation in the original UCE dataset. The mitogenomic phylogenetic reconstruction was strongly supported and revealed topological discordances in the placement of Cirrhilabrinae when compared to published nuclear phylogenies in Labridae. The newly assembled mitogenomes from our study further highlight the utility of off-target reads in TCS datasets as a cost-effective source of genomic material, facilitating broader evolutionary and conservation-based investigations into the Labridae.