The Complete Mitogenome of Two Trachinotus Species and a Phylogenetic Analysis of the Pompano Subfamily Trachinotinae

The marine fish genus Trachinotus (Carangidae: Trachinotinae) comprises species of considerable economic and ecological importance; however, a significant gap in genomic data has limited the understanding of its evolutionary history and systematics. To address this gap, we determined the complete mitochondrial genomes of two key species, Trachinotus goodei (Palometa) and Trachinotus mookalee (Indian Pompano). The mitogenome of T. goodei was sequenced from genomic DNA and assembled de novo, whereas the T. mookalee mitogenome was assembled by mining publicly available RNA-Seq data, demonstrating a cost-effective approach for expanding genomic resources. The resulting mitogenomes were 16,547 bp and 16,545 bp long, respectively, and both presented conserved gene content (13 protein-coding genes, 22 tRNAs, 2 rRNAs) and organization typical of teleost fishes. Phylogenetic analysis incorporating these new genomes with those of four other Trachinotus species was performed via a concatenated dataset of 13 protein-coding genes. Maximum likelihood and Bayesian inference recovered Trachinotus as a strongly supported monophyletic group. The phylogeny revealed a fundamental and deeply divergent split between two major clades, one comprising species from the Atlantic Ocean and the other containing species from the Indo-Pacific. This robust biogeographic partition provides compelling evidence that allopatric speciation is a primary driver of diversification within the genus.