title: Complete mitochondrial genome of Cuora trifasciata (Chinese three-striped box turtle), and a comparative analysis with other box turtles.
abstract: Cuora trifasciata has become one of the most critically endangered species in the world. The complete mitochondrial genome of C. trifasciata (Chinese three-striped box turtle) was determined in this study. Its mitochondrial genome is a 16,575-bp-long circular molecule that consists of 37 genes that are typically found in other vertebrates. And the basic characteristics of the C. trifasciata mitochondrial genome were also determined. Moreover, a comparison of C. trifasciata with Cuora cyclornata, Cuora pani and Cuora aurocapitata indicated that the four mitogenomics differed in length, codons, overlaps, 13 protein-coding genes (PCGs), ND3, rRNA genes, control region, and other aspects. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 12 protein-coding genes of the genus Cuora indicated the phylogenetic position of C. trifasciata within Cuora. The phylogenetic analysis also showed that C. trifasciata from Vietnam and China formed separate monophyletic clades with different Cuora species. The results of nucleotide base compositions, protein-coding genes and phylogenetic analysis showed that C. trifasciata from these two countries may represent different Cuora species.
authors.affiliation: Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China.
authors.forename: Xin-Cheng
authors.initials: XC
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China. Electronic address: zhuxinping_1964@163.com.
authors.forename: Xin-Ping
authors.initials: XP
authors.lastname: Zhu
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D002681:China; D003062:Codon; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D023281:Genomics; D016013:Likelihood Functions; D008928:Mitochondria / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014426:Turtles / Q000145:classification / Q000235:genetics*; D014744:Vietnam
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D012343:RNA, Transfer
keywords: Comparative mitogenomic analysis; Cuora trifasciata; Genus Cuora; Mitochondrial genome; Phylogenetic analysis