Volume 35 Issue 2
Mar.  2014
Turn off MathJax
Article Contents
Yong-Gui MA, Yuan HUANG, Fu-Min LEI. Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome. Zoological Research, 2014, 35(2): 81-91. doi: 10.11813/j.issn.0254-5853.2014.2.081
Citation: Yong-Gui MA, Yuan HUANG, Fu-Min LEI. Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome. Zoological Research, 2014, 35(2): 81-91. doi: 10.11813/j.issn.0254-5853.2014.2.081

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome

doi: 10.11813/j.issn.0254-5853.2014.2.081
  • Received Date: 2013-04-18
  • Rev Recd Date: 2013-12-23
  • Publish Date: 2014-03-08
  • 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 tRNASer (AGN) which loses the DHU arm, while tRNAPhe 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 tRNAGlu and tRNAPhe, 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.
  • loading
  • [1]
    Baker AJ, Marshall HD. 1997. Mitochondrial control region sequences as tools for understanding evolution. In: Mindell DP. Avian Molecular Evolution and Systematics. San Diego: Academic Press. 51-82.
    Barker FK, Barrowclough GF, Groth JG. 2002. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proceedings of the Royal Society B: Biological Sciences, 269(1488): 295-308.
    Burk A, Douzery EJP, Springer MS. 2002. The secondary structure of mammalian mitochondrial 16S rRNA molecules: refinements based on a comparative phylogenetic approach. Journal of Mammalian Evolution, 9(3): 225-252.
    Cerasale DJ, Dor R, Winkler DW, Lovette IJ. 2012. Phylogeny of the Tachycineta genus of New World swallows: Insights from complete mitochondrial genomes. Molecular Phylogenetics and Evolution, 63(1): 64-71.
    Dirheimer G, Keith G, Dumas F, Westhof E. 1995. Primary, Secondary and tertiary Structures of tRNAs. In: Hill WE, Dahlbert A, Garrett RA, Moore PB, Schlessinger D, Warner JR. tRNA: Structure, Biosynthesis and Function. Washington DC: American Society for Microbiology Press, 93-126.
    Eberhard JR, Wright TF, Bermingham E. 2001. Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Molecular Biology and Evolution, 18(7): 1330-1342.
    Ericson PGP, Christidis L, Irestedt M, Norman JA. 2002. Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds. Molecular Phylogenetics and Evolution, 25(1): 53-62.
    Espinosa De los Monteros A. 2003. Models of the primary and secondary structure for the 12S rRNA of birds: A guideline for sequence alignment. DNA Sequence, 14(4): 241-256.
    Gebauer A, Kaiser M. 1994. Biology and behavior of General Asiatic snow finches (Montifringilla) and mountain-steppe sparrows (Pyrgilauda). Journal of Ornithology, 135(1): 55-57.
    Gao RR, Huang Y, Lei FM. 2013. Sequencing and analysis of the complete mitochondrial genome of Remiz consobrinus. Zoological Research, 34(3): 228-237.
    Gao YK, Miao YW, Su XQ, Chi ZF, Yu B, Jiang F. 2009. A comprehensive analysis on 74 avian mitochondrial genome base compositions. Journal of Yunnan Agricultural University, 24(1): 51-58.
    Gill F, Donsker D. 2013. IOC World Bird List (version 3.3). Available at http://www.worldbirdnames.org.
    Hanada T, Suzuki T, Watanabe K. 2000. Translation activity of mitochondrial tRNA with unusual secondary structure. Nucleic Acids Symposium Series, 44(1): 249-250.
    Harrison GL, McLenachan PA, Phillips MJ, Slack KE, Cooper A, Penny D. 2004. Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Molecular Biology and Evolution, 21(6): 974-983.
    Howard R, Moore A. 1980. A Complete Checklist of the Birds of the World. Oxford: Oxford University Press, 1-613.
    Huang ZH, Liao XJ. 2011. Structure of the mitochondrial DNA control region and genetic variation of Chrysolophus pictus. Life Science Research, 2011, 15(3): 223-228.
    Ivanitskii VV. 1992. On the social behavior of david's snow finches (Pyrgilauda davidiana) and snow finches (Montifringilla nivalis). Zoologichesky Zhurnal, 70(9): 104-117.
    James HF, Ericson PGP, Slikas B, Lei FM, Gill FB, Olson SL. 2003. Pseudopodoces humilis, a misclassified terrestrial tit (Paridae) of the Tibetan Plateau: evolutionary consequences of shifting adaptive zones. Ibis, 145(2): 185-202.
    Kan XZ, Yuan J, Zhang LQ, Li X, Yu L, Chen L, Guo ZC, Yang JK. 2013. Complete mitochondrial genome of the Tristram's Bunting, Emberiza tristrami (Aves: Passeriformes): The first representative of the family Emberizidae with six boxes in the central conserved domain Ⅱ of control region. Mitochondrial DNA, 24(6): 648-650.
    Ke Y, Huang Y, Lei FM. 2010. Sequencing and analysis of the complete mitochondrial genome of Podoces hendersoni (Ave, Corvidae). Hereditas, 32(9): 951-960.
    Lei FM, Qu YH, Yin ZH. 2001. Phylogeny of species of Montifringilla based on cladistic (Passeriform: Ploceidae). Acta Zootaxonomica Sinica, 26(1): 1-7.
    Lei FM, Qu YH, Feng ZJ, Ran CZ. 2000. A tentative study on the snow finch (Montifringilla spp.) in China based on Clustering. Acta Zootaxonomica Sinica, 25(4): 467-473.
    Mayr E, Greenway JC. 1956. Sequence of Passerine families (Aves). Breviora, 58: 1-11.
    Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Systematic Biology, 48(1): 138-152.
    Mossman JA, Birkhead TR, Slate J. 2006. The whole mitochondrial genome sequence of the zebra finch (Taeniopygia guttata). Molecular Ecology Notes, 6(4): 1222-1227.
    Nilsson MA, Gullberg A, Spotorno AE, Arnason U, Janke A. 2003. Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes. Journal of Molecular Evolution, 57(Suppl. 1): S3-S12.
    Noller HF. 1984. Structure of ribosomal RNA. Annual Review of Biochemistry, 53: 119-162.
    Nylander JAA. 2004. MrModeltest v2 [Computer software and manual]. Evolutionary Biology Centre, Uppsala University.
    Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante AA. 2011. Evolution of modern birds revealed by Mitogenomics: timing the radiation and origin of major orders. Molecular Biology and Evolution, 28(6): 1927-1942.
    Posada D, Crandall KA, 1998. Modeltest: testing the model of DNA substitution. Bioinformatics, 14 (9): 817-818.
    Qian C, Ren Q, Kan X, Guo Z, Yang J, Li X, Yuan J, Qian M, Hu Q, Zhang L. 2013. Complete mitochondrial genome of the Red-billed Starling Sturnus sericeus (Aves: Passeriformes): The first representative of the family Sturnidae with a single control region. Mitochondrial DNA, 24(2): 129-131.
    Qu YH. 2006. Studies on systematic of Snow Finches (Montifringilla spp.). Master thesis, Shaanxi Normal University, Xi'an.
    Ronquist F, Huelsenbeck JP, 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12): 1572-1574.
    Ruokonen M, Kvist L. 2002. Structure and evolution of the avian mitochondrial control region. Molecular Phylogenetics and Evolution, 23(3): 422-432.
    Sibley CG, Ahlquist JA. 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution. New Haven: Yale University Press.
    Simon C, Frati F, Bekenbach A, Crespi B, Liu H, Flook P. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a complication of conserved polymerase chain reaction primers. Annuals of the Etomological Society of America, 87(6): 651-701.
    Simon C, Buckley TR, Frati F, Stewart JB, Beekenbaeh AT. 2006. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 37(1): 545-549.
    Singh TR, Shneor O, Huchon D. 2008. Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes. Molecular Biology and Evolution, 25(3): 475-477.
    Slack KE, Janke A, Penny D, Arnason U. 2003. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene, 302(1-2): 43-52.
    Slack KE, Delsuc F, McLenachan PA, Arnason U, Penny D. 2007. Resolving the root of the avian mitogenomic tree by breaking up long branches. Molecular Phylogenetics and Evolution, 42(1): 1-13.
    Sorenson MD. 2003-02-14[2010-01-08]. Avian mtDNA primers. Boston: Boston University, http://people.bu.edu/msoren/Bird.mt.Primers.pdf.
    Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution, 12(2): 105-114.
    Stamatakis A, 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21): 2688–2690.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimory methods. Molecular Biology and Evolution, 28(10): 2731-2739.
    Vawter L, Brown WM. 1993. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics, 134(2): 597-608.
    Woese CR, Magrum LJ, Gupta R, Siegel RB, Stahl DA, Kop J, Crawford N, Brosius J, Gutell R, Hogan JJ, Noller HF. 1980. Secondary structure model for bacterial 16S ribosomal RNA phylogenetic, enzymatic and chemical evidence. Nucleic Acids Research, 8(10): 2275-2293.
    Wolstenholme DR. 1992a. Animal mitochondrial DNA: structure and evolution. International Review of Cytology, 141: 173-216.
    Wolstenholme DR. 1992b. Genetic novelties in mitochondrial genomes of multicellular animals. Current Opinion in Genetics & Development, 2(6): 918-925.
    Wolstenholme DR, Okimoto R, Macfarlane JL. 1994. Nucleotide correlations that suggest tertiary interactions in the TV-replacement loop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum. Nucleic Acids Research, 22(20): 4300-4306.
    Yang C, Lei F M, Huang Y. 2010. Sequencing and analysis of the complete mitochondrial genome of Pseudopodoces humilis (Aves, Paridae). Zoological Research, 31(4): 333-344.
    Yang C, Wang QX, Huang Y, Xiao H. 2012. Analysis of the complete mitochondrial genome sequence of Larusbrunnicephalus (Aves, Laridae). Hereditas, 34(11): 1434-1446.
    Yokobori S, Pääbo S. 1995. Transfer RNA editing in land snail mitochondria. Proceedings of the National Academy of Sciences of the United States of America, 92(22): 10432-10435.
    Zheng GM. 2012. Ornithology. 2nd ed. Beijing: Science Press.
    Zhou ZJ, Ye HY, Huang Y, Shi FM. 2010. The phylogeny of Orthoptera inferred from mtDNA and description of Elimaea cheni (Tettigoniidae: Phaneropterinae) mitogenome. Journal of Genetics and Genomics, 37(5): 315-324.
  • 加载中


    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (834) PDF downloads(1917) Cited by()
    Proportional views


    DownLoad:  Full-Size Img  PowerPoint