title: Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): the first representative from the subclass Aspidochirotacea with the echinoderm ground pattern.
abstract: Complete mitochondrial genome plays an important role in the accurate revelation of phylogenetic relationships among metazoans. Here we present the complete mitochondrial genome sequence from a sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea), which is the first representative from the subclass Aspidochirotacea. The mitochondrial genome of A. japonicus is 16,096 bp in length. The heavy strand consists of 31.8% A, 20.2% C, 17.9% G, and 30.1% T bases (AT skew=0.027; GC skew=0.062). It contains thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes, and two ribosomal RNA genes. There are a total of 3793 codons in all thirteen mitochondrial PCGs, excluding incomplete termination codons. The most frequently used amino acid is Leu (15.77%), followed by Ser (9.73%), Met (8.62%), Phe (7.94%), and Ala (7.28%). Intergenetic regions in the mitochondrial genome of A. japonicus are 839 bp in total, with three relatively large regions of Unassigned Sequences (UAS) greater than 100 bp. The gene order of A. japonicus is identical to that observed in the five studied sea urchins, which confirms that the gene order shared by the two classes (Holothuroidea and Echinoidea) is a ground pattern of echinoderm mitochondrial genomes. Bayesian tree based on the cob gene supports the following relationship: (outgroup, (Crinoids, (Asteroids, Ophiuroids, (Echinoids, Holothuroids)))).
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Shen
authors.forename: Mei
authors.initials: M
authors.lastname: Tian
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Liu
authors.forename: Hanliang
authors.initials: H
authors.lastname: Cheng
authors.forename: Jie
authors.initials: J
authors.lastname: Tan
authors.forename: Xueping
authors.initials: X
authors.lastname: Meng
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Ren
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics*; D054629:Genome, Mitochondrial; D010802:Phylogeny; D012616:Sea Cucumbers / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial