Publications

Found 3 results
Filters: Author is X.Z. Kan  [Clear All Filters]
2010
X. Z. Kan, Li, X. F., Zhang, L. Q., Chen, L., Qian, C. J., Zhang, X. W., and Wang, L., Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae), vol. 9, pp. 1234-1249, 2010.
Boore JL (1999). Animal mitochondrial genomes. Nucleic Acids Res. 27: 1767-1780. http://dx.doi.org/10.1093/nar/27.8.1767 PMid:10101183 PMCid:148383   Brown GG, Gadaleta G, Pepe G, Saccone C, et al. (1986). Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192: 503-511. http://dx.doi.org/10.1016/0022-2836(86)90272-X   Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, et al. (2001). Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409: 704-707. http://dx.doi.org/10.1038/35055536 PMid:11217857   Gibb GC, Kardailsky O, Kimball RT, Braun EL, et al. (2007). Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol. Biol. Evol. 24: 269-280. http://dx.doi.org/10.1093/molbev/msl158 PMid:17062634   Haddrath O and Baker AJ (2001). Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. Biol. Sci. 268: 939-945. http://dx.doi.org/10.1098/rspb.2001.1587 PMid:11370967 PMCid:1088691   Hall AT (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symp. Ser. 41: 95-98.   Harlid A, Janke A and Arnason U (1998). The complete mitochondrial genome of Rhea americana and early avian divergences. J. Mol. Evol. 46: 669-679. http://dx.doi.org/10.1007/PL00006347 PMid:9608049   Harrison GL, McLenachan PA, Phillips MJ, Slack KE, et al. (2004). Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Mol. Biol. Evol. 21: 974-983. http://dx.doi.org/10.1093/molbev/msh065 PMid:14739240   Hazkani-Covo E, Zeller RM and Martin W (2010). Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 6: e1000834. http://dx.doi.org/10.1371/journal.pgen.1000834 PMid:20168995 PMCid:2820518   Howard R and Moore A (2003). The Howard and Moore Complete Checklist of the Birds of the World. 3rd edn. Christopher Helm, London.   L'Abbé D, Duhaime JF, Lang BF and Morais R (1991). The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J. Biol. Chem. 266: 10844-10850. PMid:1710214   Larkin MA, Blackshields G, Brown NP, Chenna R, et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404 PMid:17846036   Livezey BC and Zusi RL (2007). Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool. J. Linn. Soc. 149: 1-95. http://dx.doi.org/10.1111/j.1096-3642.2006.00293.x PMid:18784798 PMCid:2517308   Lohse M, Drechsel O and Bock R (2007). OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274. http://dx.doi.org/10.1007/s00294-007-0161-y PMid:17957369   Lowe TM and Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964. PMid:9023104 PMCid:146525   Mindell DP, Sorenson MD and Dimcheff DE (1998). Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. U. S. A. 95: 10693-10697. http://dx.doi.org/10.1073/pnas.95.18.10693 PMid:9724766 PMCid:27957   Moore WS (1995). Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49: 718-726. http://dx.doi.org/10.2307/2410325   Morgan-Richards M, Trewick SA, Bartosch-Harlid A, Kardailsky O, et al. (2008). Bird evolution: testing the Metaves clade with six new mitochondrial genomes. BMC Evol. Biol. 8: 20. http://dx.doi.org/10.1186/1471-2148-8-20 PMid:18215323 PMCid:2259304   Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, et al. (2001). Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim. Genet. 32: 380-385. http://dx.doi.org/10.1046/j.1365-2052.2001.00795.x PMid:11736810   Nishibori M, Shimogiri T, Hayashi T and Yasue H (2005). Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim Genet. 36: 367-375. http://dx.doi.org/10.1111/j.1365-2052.2005.01318.x PMid:16167978   Paton T, Haddrath O and Baker AJ (2002). Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. Biol. Sci. 269: 839-846. http://dx.doi.org/10.1098/rspb.2002.1961 PMid:11958716 PMCid:1690957   Pereira SL, Johnson KP, Clayton DH and Baker AJ (2007). Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene. Syst. Biol. 56: 656-672. http://dx.doi.org/10.1080/10635150701549672 PMid:17661233   Perna NT and Kocher TD (1995). Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41: 353-358. http://dx.doi.org/10.1007/BF01215182 PMid:7563121   Pratt RC, Gibb GC, Morgan-Richards M, Phillips MJ, et al. (2009). Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Mol. Biol. Evol. 26: 313-326. http://dx.doi.org/10.1093/molbev/msn248 PMid:18981298   Randi E and Lucchini V (1998). Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47: 449-462. http://dx.doi.org/10.1007/PL00006402 PMid:9767690   Rokas A, Williams BL, King N and Carroll SB (2003). Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804. http://dx.doi.org/10.1038/nature02053 PMid:14574403   Saccone C, Pesole G and Sbisa E (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33: 83-91. http://dx.doi.org/10.1007/BF02100199 PMid:1909377   Sambrook J and Russell DW (2001). Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York.   San Mauro D, Garcia-Paris M and Zardoya R (2004). Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene 343: 357-366. http://dx.doi.org/10.1016/j.gene.2004.10.001 PMid:15588590   Sbisa E, Tanzariello F, Reyes A, Pesole G, et al. (1997). Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205: 125-140. http://dx.doi.org/10.1016/S0378-1119(97)00404-6   Shadel GS and Clayton DA (1997). Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66: 409-435. http://dx.doi.org/10.1146/annurev.biochem.66.1.409 PMid:9242913   Shen X, Tian M, Liu Z, Cheng H, et al. (2009). Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): the first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene 439: 79-86. http://dx.doi.org/10.1016/j.gene.2009.03.008 PMid:19306915   Slack KE, Janke A, Penny D and Arnason U (2003). Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302: 43-52. http://dx.doi.org/10.1016/S0378111902010533 PMid:12527195   Slack KE, Jones CM, Ando T, Harrison GL, et al. (2006). Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol. Biol. Evol. 23: 1144-1155. http://dx.doi.org/10.1093/molbev/msj124 PMid:16533822   Slack KE, Delsuc F, McLenachan PA, Arnason U, et al. (2007). Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol. Phylogenet. Evol. 42: 1-13. http://dx.doi.org/10.1016/j.ympev.2006.06.002 PMid:16854605   Walberg MW and Clayton DA (1981). Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9: 5411-5421. http://dx.doi.org/10.1093/nar/9.20.5411 PMid:7301592 PMCid:327529   Wang C, Chen Q, Lu G, Xu J, et al. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae. Gene 424: 96-101. http://dx.doi.org/10.1016/j.gene.2008.07.011 PMid:18706492   Wolstenholme DR (1992). Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141: 173-216. http://dx.doi.org/10.1016/S0074-7696(08)62066-5   Wyman SK, Jansen RK and Boore JL (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. http://dx.doi.org/10.1093/bioinformatics/bth352 PMid:15180927   Xia X and Xie Z (2001). DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92: 371-373. http://dx.doi.org/10.1093/jhered/92.4.371 PMid:11535656
X. Z. Kan, Li, X. F., Lei, Z. P., Wang, M., Chen, L., Gao, H., and Yang, Z. Y., Complete mitochondrial genome of Cabot’s tragopan, Tragopan caboti (Galliformes: Phasianidae), vol. 9, pp. 1204-1216, 2010.
Boore JL (1999). Animal mitochondrial genomes. Nucleic Acids Res. 27: 1767-1780. http://dx.doi.org/10.1093/nar/27.8.1767 PMid:10101183 PMCid:148383   Brown GG, Gadaleta G, Pepe G, Saccone C, et al. (1986). Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192: 503-511. http://dx.doi.org/10.1016/0022-2836(86)90272-X   Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, et al. (2006). Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 22: 495-532. http://dx.doi.org/10.1111/j.1096-0031.2006.00120.x   del Hoyo J, Elliot A and Sargatal J (1994). Handbook of the Birds of the World. Vol. 2. Lynx Editions, Barcelona, 434-557.   Deng WH and Zheng GM (2004). Landscape and habitat factors affecting Cabot's tragopan Tragopan caboti occurrence in habitat fragments. Biol. Conserv. 117: 25-32. http://dx.doi.org/10.1016/S0006-3207(03)00259-3   Dyke GJ, Gulas BE and Crowe TM (2003). Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters. Zoolog. J. Linnean Soc. 137: 227-244. http://dx.doi.org/10.1046/j.1096-3642.2003.00048.x   Guan X, Silva P, Gyenai KB, Xu J, et al. (2009). The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim. Genet. 40: 134-141. http://dx.doi.org/10.1111/j.1365-2052.2008.01810.x PMid:19067672 PMCid:2664387   He L, Dai B, Zeng B, Zhang X, et al. (2009). The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Gene 435: 23-28. http://dx.doi.org/10.1016/j.gene.2009.01.001 PMid:19393190   IUCN (2009). IUCN Red List of Threatened Species. Gland, Switzerland. Available at [http://www.iucnredlist.org]. Accessed November 9, 2009.   Kumazawa Y and Nishida M (1993). Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37: 380-398. http://dx.doi.org/10.1007/BF00178868 PMid:7508516   L'Abbe D, Duhaime JF, Lang BF and Morais R (1991). The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J. Biol. Chem. 266: 10844-10850. PMid:1710214   Larkin MA, Blackshields G, Brown NP, Chenna R, et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404 PMid:17846036   Lohse M, Drechsel O and Bock R (2007). Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274. http://dx.doi.org/10.1007/s00294-007-0161-y PMid:17957369   Lowe TM and Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964. PMid:9023104 PMCid:146525   Mindell DP, Sorenson MD and Dimcheff DE (1998). An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Mol. Biol. Evol. 15: 1568-1571. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025884 PMid:12572620   Monroe BL and Sibley CG (1990). A World Checklist of Birds. Yale University Press, New Haven.   Moore WS (1995). Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49: 718-726. http://dx.doi.org/10.2307/2410325   Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, et al. (2001). Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim. Genet. 32: 380-385. http://dx.doi.org/10.1046/j.1365-2052.2001.00795.x PMid:11736810   Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, et al. (2002). Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species. J. Hered. 93: 439-444. http://dx.doi.org/10.1093/jhered/93.6.439 PMid:12642645   Nishibori M, Hayashi T and Yasue H (2004). Complete nucleotide sequence of Numida meleagris (Helmeted guineafowl) mitochondrial genome. J. Poult. Sci. 41: 259-268. http://dx.doi.org/10.2141/jpsa.41.259   Nishibori M, Shimogiri T, Hayashi T and Yasue H (2005). Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim. Genet. 36: 367-375. http://dx.doi.org/10.1111/j.1365-2052.2005.01318.x PMid:16167978   Perna NT and Kocher TD (1995). Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41: 353-358. http://dx.doi.org/10.1007/BF01215182 PMid:7563121   Quinn TW (1992). The genetic legacy of Mother Goose - phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages. Mol. Ecol. 1: 105-117. http://dx.doi.org/10.1111/j.1365-294X.1992.tb00162.x PMid:1344986   Randi E and Lucchini V (1998). Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47: 449-462. http://dx.doi.org/10.1007/PL00006402 PMid:9767690   Ruokonen M and Kvist L (2002). Structure and evolution of the avian mitochondrial control region. Mol. Phylogenet. Evol. 23: 422-432. http://dx.doi.org/10.1016/S1055-7903(02)00021-0   Russell RD and Beckenbach AT (2008). Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code. J. Mol. Evol. 67: 682-695. http://dx.doi.org/10.1007/s00239-008-9179-0 PMid:19030769 PMCid:2706983   Saccone C, Pesole G and Sbisa E (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33: 83-91. http://dx.doi.org/10.1007/BF02100199 PMid:1909377   Sambrook J and Russell DW (2001). Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York.   San Mauro D, Garcia-Paris M and Zardoya R (2004). Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene 343: 357- 366. http://dx.doi.org/10.1016/j.gene.2004.10.001 PMid:15588590   Sbisa E, Tanzariello F, Reyes A, Pesole G, et al. (1997). Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205: 125-140. http://dx.doi.org/10.1016/S0378-1119(97)00404-6   Shadel GS and Clayton DA (1997). Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66: 409-435. http://dx.doi.org/10.1146/annurev.biochem.66.1.409 PMid:9242913   Shen X, Tian M, Liu Z, Cheng H, et al. (2009a). Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): the first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene 439: 79-86. http://dx.doi.org/10.1016/j.gene.2009.03.008 PMid:19306915   Shen YY, Shi P, Sun YB and Zhang YP (2009b). Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 19: 1760-1765. http://dx.doi.org/10.1101/gr.093138.109 PMid:19617397 PMCid:2765268   Slack KE, Janke A, Penny D and Arnason U (2003). Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302: 43-52. http://dx.doi.org/10.1016/S0378111902010533 PMid:12527195   Slack KE, Delsuc F, McLenachan PA, Arnason U, et al. (2007). Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol. Phylogenet. Evol. 42: 1-13. http://dx.doi.org/10.1016/j.ympev.2006.06.002 PMid:16854605   Walberg MW and Clayton DA (1981). Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9: 5411-5421. http://dx.doi.org/10.1093/nar/9.20.5411 PMid:7301592 PMCid:327529   Wolstenholme DR (1992). Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141: 173-216. http://dx.doi.org/10.1016/S0074-7696(08)62066-5   Wyman SK, Jansen RK and Boore JL (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. http://dx.doi.org/10.1093/bioinformatics/bth352 PMid:15180927   Zhang JF, Nie LW, Wang Y and Hu LL (2009). The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA. Gene 442: 119-127. http://dx.doi.org/10.1016/j.gene.2009.04.018 PMid:19397958   Zhang Y and Zheng G (2007). A population viability analysis (PVA) for Cabot's tragopan (Tragopan caboti) in Wuyanling, south-east China. Bird Conserv. Int. 17: 151-161. http://dx.doi.org/10.1017/S0959270907000652