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

作　　者：FAN SiGang HU ChaoQun WEN Jing ZHANG LvPing 

机构地区：[1]Key Laboratory of Marine Bio-resources Sustainable Utilization, Key Laboratory of Applied Marine Biology of Guangdong Province and Chinese Academy of Sciences, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China [2]Graduate University of Chinese Academy of Sciences, Beijing 100049, China [3]Department of Biology, Zhanjiang Normal University, Zhanjiang 524048, China

出　　处：《Science China(Life Sciences)》2011年第5期434-441,共8页中国科学（生命科学英文版）

基　　金：supported by the National Key Technologies R&D Program (Grant No.2009BAB44B02);the Science and Technology Program of Guangdong Province (Grant Nos.A200901E01,A200899E02 and 2009B091300155)

摘　　要：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： Sdchopodidae： 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 （had6） and five tRNA genes （tRNAser（UcN）, tRNAGtn, tRNAAla, tRNA val, tRNAASp） 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 ex- cept 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.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.

关 键 词：complete mitochondriai DNA Stichopus horrens gene arrangement HOLOTHUROIDEA 

分 类 号：Q943[生物学—植物学] S968.9[农业科学—水产养殖]