Abstract
In this study, the complete mitochondrial genome of Salmacis sphaeroides variegate was determined on Illumina HiSeq platform. The genome was 15,770 bp in size and contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 1 control region (180 bp). The composition of A + T in S. sphaeroides mtDNA was 61.90%. Except ND6 and 6 tRNAs, the others are on the H-strand. The phylogenetic relationships of 11 species of sea urchins were analyzed using the neighbor-joining method using software MEGA 7.0. S. sphaeroides was most closely related to Temnopleurus hardwickii.
Keywords: Mitochondrial genome, sea urchins, Salmacis sphaeroides variegate
Salmacis sphaeroides variegate is a kind of sea urchin in the family Temnopleuridae. It lives in warm temperate regions and shallow waters (0–90 m). Although its nutritional value is very high (Chen et al. 2010), S. sphaeroides is not cultivated on a large scale in China. At present, the research on S. sphaeroides mainly focuses on biological development (Rahman et al. 2012, 2016). By comparing with the mitochondrial genome of other sea urchins, it provides basic data and important scientific data for the phylogenetic evolution and diversity of sea urchins. Therefore, the research on the mitochondrial whole genome of S. sphaeroides becomes very important.
Our sample was collected from Sanya, Hainan province, China (20°06′08.3″N,110°16′15.0″E). The complete mitochondrial genome of S. sphaeroides was determined using on Illumina HiSeq platform. Using SOAP denovo V2.04 software (http://soap.genomics.org.cn/), the sequence was assembled (Luo et al. 2012). DOGMA software (http://dogma.ccbb.utexas.edu/) was used to predict gene, rRNA, and tRNA contained in the genome. MEG A7.0 (Kumar et al. 2016) was used for multiple alignments. The mtDNA map of S. sphaeroides mitochondrial genome was drawn with the online tool OGDraw (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html) (Lohse et al. 2013). The specimen is stored in the Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affrairs, Dalian Ocean University (voucher number: DLOU-KLM-SU05).
The mitochondrial genome of S. sphaeroides has a total length of 15,770 bp (GenBank registration number: MK692949), including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding region with a length of 180 bp, which is consistent with the mitochondrial genome structure of the echinacea reported (Cantatore et al. 1989; Giorgi et al. 1996). The composition of A + T in S. sphaeroides mtDNA was 61.90%. Except ND6 and 6 tRNAs, the others are on the H-strand. Most protein-coding genes (10 of 13 genes) started with ATG, ATP8 with GTG, and ND4 with ATC. The termination codon of most protein-coding genes was TAG (8 of 13 genes) or TAA (3 of 13 genes). The termination codon of ND4 was TAT and the termination codon of ND1 was TTA. The size of 22 tRNA coding genes ranged from 68 to 74 bp. The largest intergenic region of the mitochondrial genome was 36 bp.
The phylogenetic relationship of 11 species of sea urchins was analyzed using the neighbor-joining method by MEGA 7.0. The results showed that the S. sphaeroides were most closely related to the Temnopleurus hardwickii. The distance between Strongylocentrotus sea urchin and S. sphaeroides was the farthest (Figure 1).
Figure 1.
Consensus neighbor-joining tree based on the complete mitochondrial sequence of S. sphaeroides and other 10 species of sea urchins. The phylogenetic tree was constructed using MEGA 5.0 software by the neighbor-joining method. The numbers at the tree nodes indicate the percentage of bootstrapping after 1000 replicates.
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
Disclosure statement
No potential conflict of interest was reported by the authors.
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