Complete mitochondrial genome sequences of a deep-sea holothurian species of the genus Scotoplanes (Elasipodida: Elpidiidae)

Abstract

Two complete and one near-complete mitochondrial genomes (mitogenomes) were determined for a deep-sea holothurian species of the genus Scotoplanes (Elpidiidae). Each sequence contains two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes, as found in most previously determined holothurian mitogenomes. The protein-coding genes use ATG or ATA as the start codon, and TAA or TAG as the stop codon. Phylogenetic reconstruction using the maximum likelihood method confirmed the sister relationship between Scotoplanes sp. and another elpidiid holothurian Peniagone sp.; the three Scotoplanes sp. specimens were recovered as a monophyletic group.

Keywords:

• Echinodermata
• Holothuroidea
• mitogenome
• sea pig

Holothurians of the family Elpidiidae (Elasipodida) are dominant deposit feeders in deep-sea communities (Gutt and Piepenburg 1991; Taylor et al. 2014). Associations with parasitic gastropods and tanaids (Alvaro et al. 2011; Takano et al. 2018), and mutualistic decapods (Barry et al. 2017) suggest their ecological importance. Species of the elpidiid genus Scotoplanes (or ‘sea pig’) are widely distributed, with S. globosa inhabiting the bathyal and abyssal depths of various sea areas (Gutt and Piepenburg 1991; Thandar 1999). Ongoing molecular and morphological studies have detected a cryptic species of S. globosa in the northeast Pacific (Barry et al. 2017). Molecular comparisons are required to improve our understanding of the diversity and evolutionary history of Scotoplanes species. Here, we sequenced the mitochondrial genomes (mitogenomes) of S. globosa-like specimens from off the coast of Japan in the northwest Pacific; hereafter the study material is referred to as Scotoplanes sp. because the sampling site is quite distant from the type locality of S. globosa (Théel 1879) and it might be a cryptic species.

One beam-trawl haul at station OT6 of the R/V Shinsei-maru cruise KS-16-18 (off Otsuchi, Iwate, Japan: 39°18′20″–19′″N, 142°49′48″54″E) yielded hundreds of Scotoplanes sp. from the muddy bottom (1672–1692 m depth; 2.2 °C). Three Scotoplanes sp. specimens (H4, H5 and H8) were preserved in pure ethanol; the sequences of short DNA fragments from the first two specimens were reported previously (Takano et al. 2018). Voucher material has been deposited at the Atmosphere and Ocean Research Institute, The University of Tokyo, Japan. Total DNA was extracted from the epidermis of each specimen by using a QIAGEN Genomic-tip 500/G. Paired-end sequencing (2 × 150 bp) was performed in an Illumina NextSeq sequencer. Bases with a quality score lower than 20 were removed from the sequence reads, and trimmed reads shorter than 127 bp were discarded by using Sickle 1.33 (Joshi and Fass 2011). The remaining reads were assembled using SPAdes 3.10.1 (Bankevich et al. 2012). Gaps in the assembled sequences were filled by Sanger-sequencing with specific primers. Finally, two complete mitogenomes (H4 and H8, DDBJ/EMBL/GenBank accession nos LC416624 and LC416626, respectively) and one near-complete mitogenome (H5, LC416625) were obtained. The assembled sequences were annotated by using the MITOS WebServer (Bernt et al. 2013); some annotations were corrected by reference to previously determined holothurian mitogenomes.

The complete Scotoplanes sp. mitogenome sequences were 15,913 bp (H4) and 15,910 bp (H8) in length, varying by the length of the noncoding region between genes encoding transfer RNAs (tRNAs) tRNA^Cys and tRNA^Gln. All three mitogenomes obtained here contained two ribosomal RNA (12S and 16S) genes, 22 tRNA genes, and 13 protein-coding genes (PCGs). The length and intraspecies variation of amino acid sequences, and the start and stop codons of each PCG are summarized in Table S1 (available on figshare: https://figshare.com/s/2c8c2a9334ea11ddae39, DOI: 10.6084/m9.figshare.7039331). By partitioned maximum likelihood analysis, the three Scotoplanes sp. specimens were recovered as a well-supported clade (bootstrap percentage [BP] = 100%; Figure 1), and a sister relationship between Scotoplanes sp. and another elpidiid species Peniagone sp. was observed (BP = 100%).

Figure 1. Maximum likelihood (ML) phylogeny of 13 holothurians based on concatenated amino acid sequences of 13 protein-coding genes (3570 positions). Scotoplanes sp. is shown in bold. Also included in the analysis was the echinoid Strongylocentrotus droebachiensis as an outgroup taxon, according to relationships among the five echinoderm classes inferred from phylogenomic analysis (Telford et al. 2014). Sequences were aligned separately for each gene by using MAFFT 7.397 (Katoh and Standley 2013) with default parameters. Ambiguously aligned positions were removed by Gblocks 0.91b (Castresana 2000); the ‘Allowed gap positions’ was set to ‘With half'. ML analysis was performed in RAxML 8.2.10 (Stamatakis 2014) using the mtREV + G model. Numbers above or below branches denote bootstrap percentages (1000 replicates). DDBJ/EMBL/Genbank accession numbers are shown for published sequences.

Acknowledgements

We are grateful to the captain, crew, and researchers of the R/V Shinsei-maru cruise KS-16-18, which is a part of the research project Tohoku Ecosystem-Associated Marine Sciences funded by the Ministry of Education, Culture, Sports, Science, and Technology, Japan. Sequence assembly was conducted by the Bioengineering Lab. Co., Ltd., Japan.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by JSPS KAKENHI Grant [no. 18H04136].