Mitochondrial Genome and Phylogenetic Analysis of Rhinogobius virgigena

Rhinogobius virgigena is a fish species of the family Gobiidae, order Perciformes. This study aims to better understand the phylogenetic status of R. virgigena within Gobiidae and the phylogenetic relations in this family. Mitochondrial DNA is maternally inherited and does not recombine; therefore, mitochondrial genomes simplify genealogical tracing and reveal phylogenetic relationships among species more clearly than nuclear genomes. Therefore, we used high-throughput sequencing to obtain a complete mitochondrial genome sequence of R. virgigena and conducted phylogenetic analyses. The R. virgigena mitochondrial genome is 16,491 bp long and its base composition shows AT preference. It comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a D loop. Protein-coding genes account for 69.3% of the complete genome. Leucine is the most abundant amino acid, whereas cysteine is the least abundant. tRNA genes account for 9.4% of the genome. Twenty-one tRNAs have a typical cloverleaf secondary structure, whereas tRNA-Ser1 lacks the dihydrouracil arm. The two rRNA genes are separated by tRNA-Val. A mitochondrial genome contains seven overlaps and 11 gaps, indicating a tight arrangement. Two phylogenetic trees constructed based on the nucleotide sequences of 13 protein-coding genes from 54 Gobiidae species using the maximum likelihood method and Bayesian inference revealed that R. virgigena is the most closely related to Rhinogobius duospilus.