Structural Characteristics of Mitochondrial Genomes of Two Species of Mackerel and Phylogenetic Analysis of Scombridae Family

<i>Scomberomorus guttatus</i> and <i>Scomberomorus commerson</i> are both important marine economic fish species worldwide, with high scientific and ecological value. In this study, the complete mitochondrial genome sequences of these two species of mackerel were obtained by using next-generation sequencing technology, with total lengths of 16,562 bp and 16,594 bp, respectively. Like most teleosts, both species possess 13 protein-coding genes, 22 <i>tRNA</i> genes, 2 <i>rRNA</i> genes, and 1 non-coding region <i>D-loop</i>. The base composition showed significant AT bias (55.1%, 53.4%) and anti-G bias (16.0%, 16.2%). In their control area, the terminal-associated sequence (TAS) was identified, and a total of three core sequences with repeated "---TACAT---ATGTA---" were found. There are typical CSB-E structures and CSB-D-like structures in the central conserved domain (CD), but no CSB-F structures have been found. Meanwhile, the CSB-2 and CSB-3 structures were identified in the conserved sequence block (CSB), but the CSB-1 structure was missing. To further investigate the phylogenetic relationships within the Scombridae family, this study conducted a comparative analysis of mitochondrial genomes from 30 Scombridae species. Phylogenetic trees encompassing 60% of the documented Scombridae species were constructed using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods. The results revealed a close evolutionary relationship between the genus <i>Scomber</i> and <i>Rastrelliger</i>, while the genus <i>Scomberomorus</i> exhibited closer affinities to <i>Thunnus</i>, <i>Euthynnus</i>, and <i>Katsuwonus</i>. At the species level, <i>Scomberomorus guttatus</i> diverged earlier from <i>Scomberomorus commerson</i>. These findings refine and update the phylogenetic relationships among Scombridae species, providing critical molecular evidence and insights for deeper exploration of their evolutionary history and genetic affinities.