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Complete mitochondrial genome of the sea cucumber Stichopus sp. and its application in the identification of this species
Author(s) -
Fan Sigang,
Hu Chaoqun,
Zhang Lvping,
Sun Hongyan,
Wen Jing,
Luo Peng
Publication year - 2012
Publication title -
aquaculture research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.646
H-Index - 89
eISSN - 1365-2109
pISSN - 1355-557X
DOI - 10.1111/j.1365-2109.2011.02934.x
Subject(s) - biology , mitochondrial dna , transfer rna , gene , genetics , phylogenetic tree , complete sequence , ribosomal rna , genome , rna
The complete sequence of mitochondrial DNA (mt DNA ) from Stichopus sp. (Echinodermata: Holothuroidea: Stichopodidae: Stichopus ) was acquired using conventional PCR and long PCR followed by cloning and sequencing. The mt DNA is a circular molecule of 16 257 bp in length, containing the set of 37 genes, including 13 protein‐coding genes ( PCG s), 22 t RNA genes and two ribosomal RNA genes. The plus strand consists of 30.9% A, 23.7% C, 16.0% G and 29.3% T bases (AT skew = 0.027; GC skew = −0.194). All 13 PCG s encode a total of 3782 amino acids and all 22 t RNA genes were predicted to be capable of folding into a clover‐leaf secondary structure. Intergenetic regions in the mitochondrial genome of Stichopus sp. contain 903 bp in total, with the largest continuous region (674 bp, AT% = 58.6) between t RNA ‐Thr and t RNA ‐Pro. Analysis of phylogenetic relationship of family Stichopodidae and genetic distances (species among the family Stichopodidae and species within Stichopus monotuberculatus group) based on the partial cox1 sequence demonstrates that Stichopus sp. from the South China Sea is a member of S. monotuberculatus complex.