The complete mitochondrial genome of Sinularia maxima Verseveldt, 1971 (Octocorallia: Alcyonacea) using next-generation sequencing

Abstract

The mitochondrial genome of Sinularia maxima was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,730 bp in length. The gene arrangements include 14 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 1 tRNA (tRNA-Met). The base composition is 30.18% A, 16.47% C, 19.35% G, and 33.99% T, with an A + T content of 64.18%. With regard to the phylogenetic analysis, members of genus Sinularia were clustered in different clades.

Keywords:

• Mitogenome
• soft coral
• Sinularia maxima
• protein-coding genes
• transfer RNA genes
• ribosomal RNA genes

The genus Sinularia May, 1898 is one of the most widespread Octocorallia soft corals has been distributed in a wide range of habitats (Fabricius and Alderslade 2001). To date, the complete mitogenome of three species of Sinularia including Sinularia ceramensis (MK292119), Sinularia cf. cruciate (NC_034318) and Sinularia peculiaris (NC_018379) have been sequenced. In the present study, the complete mitochondrial genome of Sinularia maxima Verseveldt, 1971 (GenBank: MN485891) was analyzed using next-generation sequencing.

A specimen of S. maxima was collected from the South China Sea (West Island, Sanya, Hainan province, China; 18°14′ 8.75″N, 109° 22′39.10″ E) and stored in Hainan Tropical Ocean University Museum of Zoology (NO.0001-Sm). Taxonomical status of the specimen was identified by PuCAs-mtMutS (Benayahu et al. 2018) and PuCAs-28S (Quattrini et al. 2019). The whole DNA was extracted using Rapid Animal Genomic DNA Isolation Kit (Sangon Biotech Co., Ltd., Shanghai, CN; NO. B518221). A genomic library was made by paired-end (2 × 150 bp) next-generation sequencing, using the Illumina HiSeq X-ten sequencing platform (Asem et al. 2019). FastQC programme was utilized to check quality of sequencing reads (Andrews 2010) and the sequences were annotated and assembled to the Sinularia mitochondrial genome (Sinularia ceramensis, MK292119) with Spades v3.9.0 (Bankevich et al. 2012) and bowtie v2.2.9 (Langmead and Salzberg 2012). Putative tRNA gene was established using ARWEN (http://130.235.46.10/ARWEN/) online software. All genes were annotated based on gene order on the reference mitochondrial map using BLAST analysis (https://blast.ncbi.nlm.nih.gov). Additionally, to annotate PCGs and the position of start and stop codons were re-considered.

The complete mitogenome of S. maxima was 18,730 bp in length, with 14 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs) and one transfer RNA (tRNA-Met). We found that tRNA-Met can be folded into typical clover-leaf secondary structures with 46.6% of GC content. The overall nucleotide composition of the major strand of the S. maxima mitogenome was as follows: 30.18% A, 16.47% C, 19.35% G, and 33.99% T, with a total A + T content of 64.18%.

The tRNA-Met and four protein-coding genes (COX3, ATP6, ATP8, and COX2) were located on the L strand. All PCGs began with common ATG start codon. Stop codons included eight TAG (ND1, CYTB, ND6, ND3, ND2, ND5, COX3, and COX2), five TAA (ND4L, mutS, ND4, ATP6, and ATP8) and a non-complete codons T- (COX1).

The 12S ribosomal RNA and 16S ribosomal RNA were encoded on H strand from 1583 to 2633 (1051 bp) and 9147 to 11115 (1969 bp), respectively, with 12S having a rather higher G + C content (43.58% vs. 41.24%). A single overlap and the longest gap were found between and ND2/ND5 (−13 bp) and COX2/COX1 (112 bp), respectively.

A phylogenetic analysis of four completed Sinularia mitogenomes was established based on and an outgroup (Leptogorgia capverdensis, KY553145). The concatenated dataset for nucleotides contained 14 PCGs and two ribosomal RNAs. The maximum-likelihood (ML) phylogenetic analysis was performed using the software MEGA X (Kumar et al. 2018). Regarding phylogenetic tree, Sinularia is divided into two clads including Sinularia cf. cruciate + Sinularia maxima and Sinularia peculiaris + Sinularia ceramensis (Figure 1).

Figure 1. Phylogenetic tree showing the relationship among S. maxima and other members of order genus Sinularia based on maximum-likelihood (ML) approach. Numbers behind each node denote the bootstrap support values. The GenBank accession numbers are indicated on the right side of species names.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the manuscript.

Additional information

Funding

This project was funded by a cooperative agreement provided by Hainan Province Science and Technology Department Key Research and Development Programme [ZDYF2019154], and the Science and Technology Major Project of Hainan Province under [ZDKJ2016009-3].