title: Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.
abstract: In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes COⅢ and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.
authors.affiliation: School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
authors.forename: Yong-Gui
authors.initials: YG
authors.lastname: Ma
authors.affiliation: School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China. yuanh@snnu.cn.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Fu-Min
authors.initials: FM
authors.lastname: Lei
mesh_terms: D000818:Animals; D001483:Base Sequence; D054629:Genome, Mitochondrial / Q000235:genetics*; D058977:Molecular Sequence Annotation; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D046370:Sparrows / Q000235:genetics*
chemical_list: D012335:RNA, Ribosomal; D012343:RNA, Transfer
keywords: Complete mitochondrial genome; Phylogeny; Pyrgilauda ruficollis