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Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber  Benthodytes marianensis  collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus  Benthodytes . This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs:  trnL  and  trnS ). Most of these genes are coded on the positive strand except for one protein-coding gene ( nad6 ) and five tRNA genes which are coded on the negative strand. Two putative control regions (CRs) have been found in the  B .  marianensis  mitogenome. We compared the order of genes from the 10 available holothurian mitogenomes and found a novel gene arrangement in  B .  marianensis . Phylogenetic analysis revealed that  B .  marianensis  clustered with  Peniagone  sp. YYH-2013, forming the deep-sea Elasipodida clade. Positive selection analysis showed that eleven residues (24 S, 45 S, 185 S, 201 G, 211 F and 313 N in  nad2 ; 108 S, 114 S, 322 C, 400 T and 427 S in  nad4 ) were positively selected sites with high posterior probabilities. We predict that  nad2  and  nad4  may be the important candidate genes for the further investigation of the adaptation of  B .  marianensis  to the deep-sea environment.

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Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber