title: Complete mitochondrial genome sequence and gene organization of Chinese indigenous chickens with phylogenetic considerations.
abstract: In this study, we sequenced the complete mitochondrial DNA of Chinese indigenous Jinhu Black-bone and Rugao chickens. The two chicken mitochondrial genomes were deposited in GenBank under accession Nos. KP742951 and KR347464, respectively. The complete mitochondrial genomes of Jinhu Black-bone and Rugao chickens were sequenced and found to span 16,785 and 16,786 bp, respectively, and consisted of 22 tRNA genes, two rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and one control region (D-loop). The majority of genes were positioned on the H-strand, and the ND6 and eight tRNA genes were found to be encoded on the L-strand. The mitogenomes showed a similar gene order to that of the published Gallus gallus genome, as neither included a control region. The overall base composition of the genome of the two chickens was A = 30.22/30.28%, G = 13.57/13.49%, T = 23.74/23.76%, and C = 32.48/32.48%. Nucleotide skewness of the coding strands of the two chicken genomes (AT-skew = 0.12, GC-skew = -0.41) was biased towards T and G. Phylogenetic analysis revealed 29 subspecies, and the molecular genetic relationship among the 29 subspecies was identical to that of traditional taxonomy.
authors.affiliation: State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Key Laboratory of Feed Safety and Bioavailability, Ministry of Agriculture, Beijing, China.|Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: F P
authors.initials: FP
authors.lastname: Zhao
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.|College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
authors.forename: H Y
authors.initials: HY
authors.lastname: Fan
authors.affiliation: Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China.
authors.forename: G H
authors.initials: GH
authors.lastname: Li
authors.affiliation: State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Key Laboratory of Feed Safety and Bioavailability, Ministry of Agriculture, Beijing, China.
authors.forename: B K
authors.initials: BK
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002645:Chickens / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D023061:Gene Order; D050259:Genes, Mitochondrial; D054629:Genome, Mitochondrial; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; C075526:RNA, ribosomal, 12S; D012343:RNA, Transfer