Characterization of mitochondrial genome of sea cucumber Stichopus horrens: A novel gene arrangement in Holothuroidea

Abstract

The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens (Holothuroidea: Stichopodidae: Stichopus) is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene (nad6) and five tRNA genes (tRNA Ser(UCN) , tRNA Gln , tRNA Ala , tRNA Val , tRNA Asp ) which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases (AT skew=0.025; GC skew=−0.188). A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes except nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu (16.29%), Ser (10.34%) and Phe (8.37%). All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.

Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis

“…Apart from the PC-region, there are 16 small intergenic spacers that range from 1 to 18 bp in size, totally 104 bp. In total, six overlapping areas (24 bp) were observed, in which the three notable overlaps (ATP8 and ATP6 by 7 bp, nad4 and tRNA-His by 10 bp, and tRNA-Pro and tRNA-Gln by 4 bp) were similar to other echinoderms (Fan et al 2011). Twenty-two tRNA genes were identified in the mitogenome of H. leucospilata.…”

The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep‐sea adaptive evolution of Brisingida

“…relationship and therefore have become more popular in recent years (Fan, Hu, Wen, & Zhang, 2011;Shen, Ma, Ren, & Zhao, 2009;Shen et al, 2017). Up to now, the complete mitochondrial genomes have been reported in many marine organisms, such as sea cucumber (Fan et al, 2011;Perseke et al, 2010;Scouras, Beckenbach, Arndt, & Smith, 2004;Sun, Qi, & Kong, 2010), sea urchin (Cantatore, Roberti, Rainaldi, Gadaleta, & Saccone, 1989;De Giorgi, Martiradonna, Lanave, & Saccone, 1996;Qureshi & Jacobs, 1993), brittle star (Perseke et al, 2008(Perseke et al, , 2010Scouras et al, 2004;Smith, Arndt, Gorski, & Fajber, 1993), sea lily (Perseke et al, 2008;Scouras & Smith, 2006), shellfish (Plazzi, Ribani, & Passamonti, 2013;Ren, Liu, Jiang, Guo, & Liu, 2010), and crab (Liu & Cui, 2010;Yang & Yang, 2008).…”

Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers

“…Because of its rapid evolution and the lack of genetic recombination, mtDNA can provide important information about rearrangement laws and phylogenetic relationship [8]. The mtDNA contains 37 genes, including 13 proteincoding genes (PCGs), 2 rRNA genes and 22 tRNA genes [9,10]. At present, many studies have investigated the phylogeny and evolution of echinoderms.…”