Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Sci China Life Sci. 2011 May;54(5):434-41. doi: 10.1007/s11427-011-4168-8. Epub 2011 May 15.
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.
海参完整的线粒体 DNA 序列包含了用于后生动物系统发育分析的有用信息。本研究提供了糙海参（Holothuroidea: Stichopodidae: Stichopus）的完整线粒体 DNA 序列。该序列是通过正常和长 PCR 确定的。糙海参的线粒体基因组是一个长 16257bp 的圆形分子，由 13 个蛋白质编码基因、2 个核糖体 RNA 基因和 22 个转移 RNA 基因组成。除了一个蛋白质编码基因（nad6）和五个 tRNA 基因（tRNA（Ser（UCN））、tRNA（Gln）、tRNA（Ala）、tRNA（Val）、tRNA（Asp））外，大多数基因都编码在重链上，这些基因编码在轻链上。重链的组成是 30.8%的 A、23.7%的 C、16.2%的 G 和 29.3%的 T 碱基（AT 倾斜=0.025；GC 倾斜=-0.188）。由于其位置和 AT 丰富度，鉴定出一个 675bp 的非编码区为推定的控制区。基因间间隔大小从 1 到 50bp，总计 227bp。在 11 个基因中，存在总共 25 个重叠核苷酸，大小从 1 到 10bp。所有 13 个蛋白质编码基因都以 ATG 起始。除了 nad3 和 nad4 使用 TAG 作为终止密码子外，所有蛋白质编码基因都使用 TAA 作为终止密码子。最常用的氨基酸是亮氨酸（16.29%）、丝氨酸（10.34%）和苯丙氨酸（8.37%）。所有 tRNA 基因都有可能折叠成典型的三叶草二级结构。我们还比较了现有的 5 种海参的线粒体 DNA 中基因的顺序，发现糙海参的线粒体 DNA 中存在一种新的基因排列。
