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

• Published in: PloS one 2018-11, Vol.13 (11), p.e0208051-e0208051
• Main Authors: Mu, Wendan, Liu, Jun, Zhang, Haibin
• Format: Article
• Language: English
• Subjects: Acclimatization; Adaptation; Animals; Base Composition; Benthodytes; Biological evolution; Biology and life sciences; Botocudo marianensis; Clinical coding; Computer and Information Sciences; Cytochrome; Deep sea; Deep sea environments; Dehydrogenases; Deoxyribonucleic acid; DNA; DNA, Mitochondrial - genetics; Elasipodida; Evolution & development; Gene Order; Genes; Genetic aspects; Genetic research; Genome, Mitochondrial; Genomes; Genomics; Holothuroidea; Mitochondria; Mitochondrial DNA; Mitochondrial Proteins - genetics; Molecular evolution; Morphology; Novels; Nucleotide sequence; Phylogenetics; Phylogeny; Positive selection; Proteins; Research and Analysis Methods; Ribonucleic acid; Ribosomal RNA; RNA; RNA, Ribosomal - genetics; RNA, Transfer - genetics; rRNA; Sea cucumbers; Sea Cucumbers - genetics; Sea Cucumbers - physiology; Selection, Genetic; Shallow water; Transfer RNA; tRNA
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0208051

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.