Mitochondrial genome assembly and comparative mitogenomics of five snake mackerels (Perciformes, Gempylidae).

The Gempylidae family, also known as snake mackerels, is a large and diverse suborder of fishes in the Perciformes. There are 24 species in the family, which are divided into 16 genera. A number of these species are economically important. Despite substantial research on this family using morphology-based and genetic methods, taxonomic categorization in this group remains a mystery. In this study, we demonstrate the utility of mitogenomes in resolving complicated taxonomic relationships in the gempylids. Using the next-generation sequencing (NGS) platform Ion-Torrent, we characterized the entire mitogenomes of Neoepinnula minetomai (Nakayama, Kimura, and Endo, 2014), Neoepinnula orientalis (Gilchrist & von Bonde, 1924), Rexea antefurcata (Parin, 1989), Rexea prometheoides (Bleeker, 1856), and Thyrsites atun (Euphrasen, 1791). Then, we conducted comparative analyses examining codon usage, nucleotide composition, gene content, and gene-order arrangement. We also looked for signs of selection in the mitogenomes. Finally, we constructed a phylogenetic trees using Bayesian Inference and Maximum-Likelihood methods and estimated time since divergence of the Gempylidae family using 13 protein-coding genes. The input data (and output) for molecular divergence dating, maximum-likelihood tree inference, and Bayesian inference, as well as input data for selection analyses, are all included in this publication.