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PLoS One
2018 Nov 30;1311:e0208051. doi: 10.1371/journal.pone.0208051.
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Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber.
Mu W
,
Liu J
,
Zhang H
.
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.
Fig 1. Genome map and annotation of Benthodytes marianensis complete mitochondrial genome.Genes out of the circle encode on positive strand (direction 5’→3’) and genes inner of the circle encode on negative strand (direction 3’→5’). Genes for protein coding genes and rRNAs are shown with standard abbreviation. Genes for tRNAs are designated by a single letter for the corresponding amino acid with two leucine tRNAs and two serine tRNAs differentiated by numerals.
Fig 2. A+T% vs AT skew (a) and G+C% vs GC skew (b) in the 56 echinoderm mitochondrial genomes.Values are calculated on the positive strand for the full length of the mitogenomes. The X-axis provides the skew values, while the Y axis provides the A+T/ G+C values. Numbers and names of species are colored according to their taxonomic placement (see more information of these species in S5 Table).
Fig 3. Codon usage (A) and the relative synonymous codon usage (RSCU) (B) of Benthodytes marianensis mitogenome.Numbers to the left refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the X-axis.
Fig 4. Phylogenetic trees based on the concatenated amino acid of 13 protein-coding genes.The branch lengths are determined with ML analysis. The Strongylocentrotus purpuratus and Paracentrotus lividus are used as outgroup. In BI and ML trees, the first number at each node is Bayesian posterior probability and the second number is the bootstrap probability of ML analyses. The red dot highlights the species sequenced in this study.
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