High-altitude adaptation of Tibetan chicken from MT-COI and ATP-6 perspective

References

• Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA. (2012). NDUFA4 is a subunit of complex IV of the mammalian electron transport chain. Cell Metab 16:378–86
   PubMed Web of Science ®Google Scholar
• Bao H, Zhao C, Li J, Wu C. (2008a). Sequencing and alignment of mitochondrial genomes of Tibetan chicken and two lowland chicken breeds. Sci China C Life Sci 51:47–51
   PubMedGoogle Scholar
• Bao H, Zhao C, Li J, Zhang H, Wu C. (2007). A comparison of mitochondrial respiratory function of Tibet chicken and Silky chicken embryonic brain. Poult Sci 86:2210–15
   PubMed Web of Science ®Google Scholar
• Bao H, Zhao C, Zhang L, Li J, Wu C. (2008b). Single-nucleotide polymorphisms of mitochondrially coded subunit genes of cytochrome c oxidase in five chicken breeds. Mitochondrial DNA 19:461–4
   PubMed Web of Science ®Google Scholar
• Baracca A, Barogi S, Carelli V, Lenaz G, Solaini G. (2000). Catalytic activities of mitochondrial ATP synthase in patients with mitochondrial DNA T8993G mutation in the ATPase 6 gene encoding subunit a. Biol J Chem 275:4177–82
   Web of Science ®Google Scholar
• Barrett RD, Hebert PD. (2005). Identifying spiders through DNA barcodes. Can J Zool 83:481–91
   Web of Science ®Google Scholar
• Beattie J, Smith AH. (1975). Metabolic-adaptation of the chick embryo to chronic hypoxia. Am J Physiol 228:1346–50
   PubMed Web of Science ®Google Scholar
• Bosco MC, Pierobon D, Blengio F, Raggi F, Vanni C, Gattorno M, Eva A, et al. (2001). Hypoxia modulates the gene expression profile of immunoregulatory receptors in human mature dendritic cells: Identification of TREM-1 as a novel hypoxic marker in vitro and in vivo. Blood 117:2625–39
   Web of Science ®Google Scholar
• Brilmayer T. (1983). Effects of hypoxia on oxygen affinity, hemoglobin pattern, and blood volume of early chicken embryos. Am J Physiol 244:R733–41
   PubMed Web of Science ®Google Scholar
• Brower AV. (2006). Problems with DNA barcodes for species delimitation: ‘Ten species’ of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Syst Biodivers 4:127–32
   Web of Science ®Google Scholar
• Brown W. (1983). Evolution of animal mitochondrial DNA. Evol Genes Prot 1:62–88
   Google Scholar
• Burton G, Palmer M. (1992). Development of the chick chorioallantoic capillary plexus under normoxic and normobaric hypoxic and hyperoxic conditions: A morphometric study. J Exp Zool 262:291–8
   PubMedGoogle Scholar
• Cao SY, Wu XB, Yan P, Hu YL, Su X, Jiang ZG. (2006). Complete nucleotide sequences and gene organization of mitochondrial genome of Bufo gargarizans. Mitochondrion 6:186–93
   PubMed Web of Science ®Google Scholar
• Capaldi RA. (1990). Structure and function of cytochrome c oxidase. Annu Rev Biochem 59:569–96
   PubMed Web of Science ®Google Scholar
• Crossley DA, Altimiras J. (2005). Cardiovascular development in embryos of the American alligator Alligator mississippiensis: Effects of chronic and acute hypoxia. Exp J Biol 208:31–9
   PubMed Web of Science ®Google Scholar
• de Vries DD, van Engelen BG, Gabreëls FJ, Ruitenbeek W, van Oost BA. (1993). A second missense mutation in the mitochondrial ATPase 6 gene in Leigh's syndrome. Ann Neurol 34:410–12
   PubMed Web of Science ®Google Scholar
• Dewey R, Levings CS, Timothy D. (1985). Nucleotide sequence of ATPase subunit 6 gene of maize mitochondria. Plant Physiol 79:914–19
   PubMed Web of Science ®Google Scholar
• Dzialowski EM, von Plettenberg D, Elmonoufy NA, Burggren WW. (2002). Chronic hypoxia alters the physiological and morphological trajectories of developing chicken embryos, Comp Biochem Physiol A Mol Integr Physiol 131:713–24
   PubMed Web of Science ®Google Scholar
• Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AV, Mallet J, Jiggins CD. (2007). Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proc R Soc B 274:2881–9
   PubMed Web of Science ®Google Scholar
• Enns R, Criddle R. (1977). Investigation of the structural arrangement of the protein subunits of mitochondrial ATPase. Arch Biochem Biophys 183:742–52
   PubMed Web of Science ®Google Scholar
• Fan L, Yao YG. (2011). MitoTool: A web server for the analysis and retrieval of human mitochondrial DNA sequence variations. Mitochondrion 11:351–6
   PubMed Web of Science ®Google Scholar
• Ferguson-Miller S, Babcock GT. (1996). Heme/copper terminal oxidases. Chem Rev 96:2889–908
   PubMed Web of Science ®Google Scholar
• Golding GB, Dean AM. (1998). The structural basis of molecular adaptation. Mol Biol Evol 15:355–69
   PubMed Web of Science ®Google Scholar
• Grant RA, Linse K. (2009). Barcoding Antarctic biodiversity: Current status and the CAML initiative, a case study of marine invertebrates. Polar Biol 32:1629–37
   Web of Science ®Google Scholar
• Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 103:968–71
   PubMed Web of Science ®Google Scholar
• Hao Z, Changxin W, Yangzom C. (2006). Hatchability of miniature laying chicken and its hybrids at high altitude. Scientia Agricultura Sinica 39:1507–10
   Google Scholar
• Harris AL. (2002). Hypoxia — A key regulatory factor in tumour growth. Nat Rev Cancer 2:38–47
   PubMed Web of Science ®Google Scholar
• Hausmann A, Haszprunar G, Hebert PD. (2011a). DNA barcoding the geometrid fauna of Bavaria (Lepidoptera): Successes, surprises, and questions. PLoS One 6:e17134
   PubMed Web of Science ®Google Scholar
• Havermans C, Nagy ZT, Sonet G, De Broyer C, Martin P. (2011b). DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea). Deep-Sea Res PT II 58:230–41
   Web of Science ®Google Scholar
• Hebert PD, Penton EH, Burns JM, Janzen DH, Hallwachs W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–17
   PubMed Web of Science ®Google Scholar
• Hebert PD, Stoeckle MY, Zemlak TS, Francis CM. (2004b). Identification of birds through DNA barcodes. PLoS Biol 2:e312
   PubMed Web of Science ®Google Scholar
• Jiang J, Zhou K. (2000). Evolutionary relationships among Chinese ranid frogs inferred from mitochondrial DNA sequences of 12S rRNA gene. Acta Zool Sinica 47:38–44
   Google Scholar
• Kapur RP. (2003). Emery and Rimoin's principles and practice of medical genetics. Pediatr Dev Pathol 6:204–5
   Google Scholar
• Kerr KC, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PD. (2007). Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes 7:535–43
   PubMed Web of Science ®Google Scholar
• Lamminen T, Majander A, Juvonen V,Wikström M, Aula P, Nikoskelainen E, Savontous M. (1995). A mitochondrial mutation at nt 9101 in the ATP synthase 6 gene associated with deficient oxidative phosphorylation in a family with Leber hereditary optic neuroretinopathy. Am Hum J Genet 56:1238–40
   PubMed Web of Science ®Google Scholar
• Li M, Zhao C. (2009). Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue. Sci China C Life Sci 52:284–95
   PubMedGoogle Scholar
• Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–52
   PubMed Web of Science ®Google Scholar
• Liu B. (2004). Thinking about the use of Tibetan chicken. China Poul 26:49–51
   Google Scholar
• Lovette IJ, Engstrom RT. (2004). Molecular markers, natural history, and evolution. The Auk 121:1298–9
   Google Scholar
• Mabon ME, Mao X, Jiao Y, Scott BA, Crowder CM. (2009). Systematic identification of gene activities promoting hypoxic death. Genetics 181:483–96
   PubMed Web of Science ®Google Scholar
• Macino G, Tzagoloff A. (1980). Assembly of the mitochondrial membrane system: Sequence analysis of a yeast mitochondrial ATPase gene containing the oli-2 and oli-4 loci. Cell 20:507–17
   PubMed Web of Science ®Google Scholar
• Majander A, Lamminen T, Juvonen V, Aula P, Nikoskelainen E, M.-Savontaus L, Wikström M. (1997). Mutations in subunit 6 of the F1 F0–ATP synthase cause two entirely different diseases. FEBS Lett 412:351–4
   PubMed Web of Science ®Google Scholar
• McCutcheon IE, Metcalfe J, Metzenberg AB, Ettinger T. (1982). Organ growth in hyperoxic and hypoxic chick embryos. Respir Physiol 50:153–63
   PubMedGoogle Scholar
• Miller S, Dykes D, Polesky H. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215
   PubMed Web of Science ®Google Scholar
• Murphy M, Roberts H, Choo WM, Macreadie I, Marzuki S, Lukins HB, Linnane AW. (1980). Biogenesis of mitochondria Oli2 mutations affecting the coupling of oxidation to phosphorylation in Saccharomyces cerevisiae. Biochim Biophys Acta 592:431–44
   PubMed Web of Science ®Google Scholar
• Nijtmans LG, Henderson NS, Attardi G, Holt IJ. (2001). Impaired ATP synthase assembly associated with a mutation in the human ATP synthase subunit 6 gene. Biol J Chem 276:6755–62
   Web of Science ®Google Scholar
• Nikoskelainen E, Savontaus M, Huoponen K, Antila K, Hartiala J. (1994). Pre-excitation syndrome in Leber's hereditary optic neuropathy. Lancet 344:857–8
   PubMed Web of Science ®Google Scholar
• Park DS, Foottit R, Maw E, Hebert PD. (2011). Barcoding bugs: DNA-based identification of the true bugs (Insecta: Hemiptera: Heteroptera). PLoS one 6:e18749
   PubMed Web of Science ®Google Scholar
• Petros JA, Baumann AK, E. Ruiz-Pesini, Amin MB, Sun CQ, Hall J, Lim S, et al. (2005). mtDNA mutations increase tumorigenicity in prostate cancer. Proc Natl Acad Sci USA 102:719–24
   PubMed Web of Science ®Google Scholar
• Rodgers ND, Wang Z, Kiledjian M. (2002). Regulated alpha-globin mRNA decay is a cytoplasmic event proceeding through 3′-to-5′exosome-dependent decapping. RNA 8:1526–37
   PubMed Web of Science ®Google Scholar
• Scott GR, Schulte PM, Egginton S, Scott AL, Richards JG, Milsom WK. (2011). Molecular evolution of cytochrome c oxidase underlies high-altitude adaptation in the bar-headed goose, Mol Biol Evol 28:351–63
   PubMed Web of Science ®Google Scholar
• Semenza GL. (2000). HIF-1: Mediator of physiological and pathophysiological responses to hypoxia. J Appl Physiol 88:1474–80
   PubMed Web of Science ®Google Scholar
• Smith MA, Fisher BL, Hebert PD. (2005). DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: The ants of Madagascar. Phil Trans R Soc B 360:1825–34
   PubMed Web of Science ®Google Scholar
• Stock MK, Metcalfe J. (1986). Modulation of growth and metabolism of the chick embryo by a brief (72-hr) change in oxygen availability. J Exp Zool ( Supplement: published under auspices of the American Society of Zoologists and the Division of Comparative Physiology and Biochemistry/the Wistar Institute of Anatomy and Biology) 1:351–6
   Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9
   PubMed Web of Science ®Google Scholar
• Todd RD, Douglas MG. (1981). A model for the structure of the yeast mitochondrial adenosine triphosphatase complex. Biol J Chem 256:6984–9
   Web of Science ®Google Scholar
• Tulinius MH, Houshmand M, N.-Larsson G, Holme E, Oldfors A, Holmberg E, Wahlström J. (1995). De novo mutation in the mitochondrial ATP synthase subunit 6 gene (T8993G) with rapid segregation resulting in Leigh syndrome in the offspring. Hum Genet 96:290–4
   PubMed Web of Science ®Google Scholar
• Villamor E, Kessels CG, Ruijtenbeek K, Van Suylen RJ, Belik J, De Mey JG, Blanco CE. (2004). Chronic in ovo hypoxia decreases pulmonary arterial contractile reactivity and induces biventricular cardiac enlargement in the chicken embryo. Am J Physiol Regul Integr Comp Physiol 287:R642–51
   PubMed Web of Science ®Google Scholar
• Waggoner SA, Liebhaber SA. (2003). Regulation of α-globin mRNA stability. Exp Biol Med 228:387–95
   PubMed Web of Science ®Google Scholar
• Wang Z, Yonezawa T, Liu B, Ma T, Shen X, Su J, Guo S, et al. (2011). Domestication relaxed selective constraints on the yak mitochondrial genome. Mol Biol Evol 28:1553–6
   PubMed Web of Science ®Google Scholar
• Wangensteen O, Rahn H, Burton R, Smith AH. (1974). Respiratory gas exchange of high altitude adapted chick embryos. Respir Physiol 21:61–70
   PubMedGoogle Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. (2005). DNA barcoding Australia's fish species. Phil Trans R Soc B 360:1847–57
   PubMed Web of Science ®Google Scholar
• Wideman R, Erf G, Chapman M, Wang W, Anthony N, Xiaofang L. (2002). Intravenous micro-particle injections and pulmonary hypertension in broiler chickens: Acute post–injection mortality and ascites susceptibility. Poult Sci 81:1203–17
   PubMed Web of Science ®Google Scholar
• Witt JD, Threloff DL, Hebert PD. (2006). DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: Implications for desert spring conservation. Mol Ecol 15:3073–82
   PubMed Web of Science ®Google Scholar
• Wu X, Wang Y, Zhou K, Zhu W, Nie J, Wang C. (2003). Complete mitochondrial DNA sequence of Chinese alligator, Alligator sinensis, and phylogeny of crocodiles. Chin Sci Bull 48:2050–4
   Web of Science ®Google Scholar
• Xu RF, Li K, Chen GH, Qiangba Y, Zhang YB, Lin L, Fan B, Liu B. (2005). Genetic variation within exon 2 of the MHC B-LB//gene in Tibetan chicken. Yi Chuan Xue Bao 32:1136–46
   PubMedGoogle Scholar
• Zhou S, Olson JS, Fabian M, Weiss MJ, Gow AJ. (2006). Biochemical fates of α hemoglobin bound to α hemoglobin-stabilizing protein AHSP. Biol J Chem 281:32611–18
   Web of Science ®Google Scholar