The Complete Mitochondrial Genome of the Deep-Dwelling Goby Suruga fundicola (Teleostei, Gobiidae) Reveals Evidence of Recombination in the Control Region

<i>Suruga fundicola</i>, one of the few known deep-dwelling gobies, is found in Japan, South Korea, and China. Owing to the limited availability of specimens, little is known about its mitogenome characterization, phylogenetic relationship, and adaptive evolution. In this study, we sequenced four complete mitogenomes using the DNBSEQ platform and Sanger sequencing. The mitogenomes in length ranged from 17,138 to 17,352 bp, primarily due to the variation in the number of long tandem repeat (LTR) sequences within variable region 3 (VR3). Although the gene composition and arrangement of the <i>S. fundicola</i> mitogenome are largely consistent with those of other gobies, we identified an expansion of the <i>ND2</i> gene (78 bp), and an unexpected noncoding region (NC, 35 bp) located between the <i>ND2</i> and <i>tRNA^trp</i> genes. To further investigate the variation in VR3, we sequenced this region in all nineteen individuals with the Sanger sequencing method. We detected eight distinct LTR types, containing one-three mutation sites, which formed ten different VR3 patterns. Most VR3 patterns (14/19) consisted of a single type of pure LTR, while the remaining five exhibited heterogeneous patterns composed of two different LTRs. Notably, in LTR types T1 and T3, which co-occur in heterogeneous patterns P1 and P9, we found their respective pure patterns (P2-3 and P7). Recombination provides a better, more plausible mechanism for generating the heterogeneity patterns than slipped-strand mispairing, which better explains the homogeneous LTR expansions. These findings provide evidence of recombination in the control region of a vertebrate mitogenome. A phylogenetic analysis confirmed that <i>S. fundicola</i> has a close relationship with <i>Am. hexanema</i> and <i>C. stigmatias</i>. Compared to five shallow-water species of the AcanthogobiusGroup, the deep-dwelling goby <i>S. fundicola</i> was found to be under stronger purifying selection. Within its mitochondrial protein-coding genes (PCGs), <i>ND2</i> and <i>ND6</i> genes were subject to stronger purifying selection than the others. Additionally, four genes showed signs of selection sites with high credibility (one in <i>ATP6</i>, <i>ND3</i>, and <i>ND4</i>; eight in <i>ND2</i>). This study provides valuable genomic resources for <i>S. fundicola</i> and enhances our understanding of the phylogenetic relationship, mitogenome recombination, and adaptive evolution of the goby.