Complete sequence of mitochondrial DNA of a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae).

One complete mitochondrial genome (mitogenome) was determined for a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae). The mitochondrial genome size of the sea cucumber was 15,920 bp. The sequence contains 2 ribosomal RNA genes (12S and 16S), 22 transfer RNA genes, and 13 protein-coding genes, as found in most previously determined holothurian mitogenomes. The A + T content of the complete mitochondrial genome sequence was 64.45%. The base composition showed a tendency of AT. The resulted maximum likelihood (ML) tree of Holothuroidea supported that Synallactes sp. is a species of Synallactida.

In recent years, with the development of navigation technology, the resources of deep-sea species of Echinodermata have been discovered continuously, which proves that the Echinodermata are important dominant species in the deep-sea, and indicates that deep-sea echinoderms contain important anti-stress gene resources (Solís-Marín 2005; Xiao et al. 2018). Therefore, it is of great significance to explore the germplasm resources of Echinodermata, especially sea cucumbers (Holothuroidea), for the industrialization of sea cucumbers. Extant holothuroids fall into two main clades: Apodida and Actinopoda. Within the latter taxon, Pneumonophora and Elasipodida are recognized, as well as a series of smaller clades within Pneumonophora: Holothuriida and Neoholothuriida (containing Molpadida, Persiculida, Synallactida, and Dendrochirotida) (Miller et al. 2017). The recently named order Synallactida (Miller et al. 2017) includes the family Synallactidae Ludwig, 1894, which is one of the least studied groups of sea cucumbers (Gebruk et al. 2012). Here, we sequenced the mitochondrial genomes (mitogenomes) of a deep-sea sea cucumber sample of the genus Synallactes. In order to provide theoretical basis and scientific guidance for the utilization and development of echinoderm resources in the deep sea, mitochondrial gene composition, biological evolution, and molecular identification were studied.

The sample of this experiment was collected by the ‘KEXUE’ marine scientific research vessel in 2014, which was built by the Institute of Oceanology, Chinese Academy of Sciences. The collection location was the western Pacific Ocean (137°48′E, 8°54′N) with a water depth of 1062 m. The sample was deposited at the Marine Biological Museum (MBM), Institute of Oceanology of the Chinese Academy of Sciences (IOCAS), in Qingdao. The voucher number is MBM286683. Total DNA was extracted by using OMEGA Mollusk DNA Kit. The genome was sequenced by BGISEQ-500 method. The type of sequencing was PE100 and the length of the inserted fragment was 250 bp. The remaining reads were assembled using NOVOplasty. ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and BLASTx were used to determine the protein-coding genes (PCGs) using the invertebrate mitochondrial genetic code. The positions of transfer RNA (tRNA) genes were localized by ARWEN (Laslett and Canbäck 2008) and DOGMA (Wyman et al. 2004) using the invertebrate mitochondrial genetic code and the default search mode.

The complete mitogenome sequence was 15,913 bp in length submitted in GenBank (accession no. MT559281). The complete mitogenome contained 2 ribosomal RNA genes (12S and 16S), 22 tRNA genes, and 13 PCGs. The A + T content of the complete mitochondrial genome sequence was 64.45%. The base composition showed a tendency of high AT, which was similar with Apostichopus japonicus tested by Shen et al. (2009).

A maximum likelihood phylogenetic tree of nine species in the class Holothuroidea and the two-outgroup species was constructed based on the concatenated nucleic acid of 13 PCGs in Holothuroidea (Figure 1). The result supported that all the species of Synallactida formed a monophyletic clade and outgroup has a distant relationship with Synallactida, Dendrochirotida, and Holothuriida.

Figure 1.

Phylogenetic trees based on the concatenated nucleic acid of 13 protein-coding genes. The branch lengths are determined with ML analysis.