The first complete mitogenome of the South China deep-sea giant isopod sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods.

In this study, the complete mitochondrial (mt) genome sequence of the South China deep-sea giant isopod sp. was determined, and this study is the first to explore in detail the mt genome of a deep-sea member of the order Isopoda. This species belongs to the genus , the members of which are saprophagous residents of the deep-sea benthic environment; based on their large size, is included in the "supergiant group" of isopods. The mt genome of sp. is 14,965 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date. Although the overall genome organization is typical for metazoans, the mt genome of sp. shows a number of derived characters, such as an inversion of 10 genes when compared to the pancrustacean ground pattern. Rearrangements in some genes (e.g., , , and ) are shared by nearly all isopod mt genomes analyzed thus far, and when compared to the putative isopod ground pattern, five rearrangements were found in sp. Two tRNAs exhibit modified secondary structures: The TΨC arm is absent from , and lacks the DHU. Within the class Malacostraca, arm loss is only found in other isopods. Phylogenetic analysis revealed that sp. (Cymothoida) and (Sphaeromatidea) form a single clade, although it is unclear whether Cymothoida is monophyletic or paraphyletic. Moreover, the evolutionary rate of sp. (dN/dS [nonsynonymous mutational rate/synonymous mutational rate] = 0.0705) is the slowest measured to date among Cymothoida, which may be associated with its relatively constant deep-sea environment. Overall, our results may provide useful information for understanding the evolution of deep-sea Isopoda species.