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

Wendan Mu,Jun Liu,Haibin Zhang,Paolo Ruggeri

doi:10.1371/journal.pone.0208051

Abstract

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.

Highlights

Holothuroids, known as sea cucumbers, are an abundant and diverse group, which are one of the five extant echinoderm classes
We described the complete mitochondrial genome of B. marianensis, and identified its base composition, codon usage, gene arrangement, and phylogenetic relationships
A chi-square test with 1 d. f. demonstrated that the A+T content of B. marianensis mitogenome is significantly different from other holothurians (p < 0.01) (Table 1)

Summary

Introduction

Holothuroids, known as sea cucumbers, are an abundant and diverse group, which are one of the five extant echinoderm classes. It includes more than 1400 species around the world [1]. They are present in diverse marine environments ranging from the shallow waters to the deepest oceanic trench [2]. Despite their diversity and abundance, our understanding of the higher-level phylogenetic relationships and evolution of Holothuroidea remains limited. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

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