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Volumn 5, Issue , 2015, Pages

Donkey genome and insight into the imprinting of fast karyotype evolution

(35)  Huang, Jinlong a   Zhao, Yiping a   Bai, Dongyi a   Shiraigol, Wunierfu a   Li, Bei a   Yang, Lihua a   Wu, Jing a   Bao, Wuyundalai a   Ren, Xiujuan a   Jin, Burenqiqige a   Zhao, Qinan a   Li, Anaer a   Bao, Sarula a   Bao, Wuyingga a   Xing, Zhencun a   An, Aoruga a   Gao, Yahan a   Wei, Ruiyuan a   Bao, Yirugeletu a   Bao, Taoketao a   more..


Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

EID: 84941786972     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14106     Document Type: Article
Times cited : (32)

References (52)
  • 1
    • 41649119205 scopus 로고    scopus 로고
    • Domestication of the donkey: Timing, processes, and indicators
    • Rossel, S. et al. Domestication of the donkey: timing, processes, and indicators. Proc. Natl. Acad. Sci. USA 105, 3715-3720 (2008).
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 3715-3720
    • Rossel, S.1
  • 2
    • 2942700061 scopus 로고    scopus 로고
    • African origins of the domestic donkey
    • Beja-Pereira, A. et al. African origins of the domestic donkey. Science 304, 1781 (2004).
    • (2004) Science , vol.304 , pp. 1781
    • Beja-Pereira, A.1
  • 4
    • 0024548624 scopus 로고
    • Factors determining the digestive efficiency of the domesticated donkey (Equus asinus asinus)
    • Izraely, H., Choshniak, I., Stevens, C. E., Demment, M. W. & Shkolnik, A. Factors determining the digestive efficiency of the domesticated donkey (Equus asinus asinus). Q. J. Exp. Physiol. 74, 1-6 (1989).
    • (1989) Q. J. Exp. Physiol. , vol.74 , pp. 1-6
    • Izraely, H.1    Choshniak, I.2    Stevens, C.E.3    Demment, M.W.4    Shkolnik, A.5
  • 5
    • 39749101227 scopus 로고    scopus 로고
    • Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla
    • Trifonov, V. A. et al. Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla. Chromosome Res. 16, 89-107 (2008).
    • (2008) Chromosome Res. , vol.16 , pp. 89-107
    • Trifonov, V.A.1
  • 7
    • 84901001655 scopus 로고    scopus 로고
    • Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype
    • Huang, J. et al. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype. Sci. Rep. 4, 4958 (2014).
    • (2014) Sci. Rep. , vol.4 , pp. 4958
    • Huang, J.1
  • 9
    • 33646839266 scopus 로고    scopus 로고
    • Evolutionary movement of centromeres in horse, donkey, and zebra
    • Carbone, L. et al. Evolutionary movement of centromeres in horse, donkey, and zebra. Genomics 87, 777-782 (2006).
    • (2006) Genomics , vol.87 , pp. 777-782
    • Carbone, L.1
  • 10
    • 84892877574 scopus 로고    scopus 로고
    • The tiger genome and comparative analysis with lion and snow leopard genomes
    • Cho, Y. S. et al. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat. Commun. 4, 2433 (2013).
    • (2013) Nat. Commun. , vol.4 , pp. 2433
    • Cho, Y.S.1
  • 11
    • 84883459272 scopus 로고    scopus 로고
    • Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator
    • Wan, Q. H. et al. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Res. 23, 1091-1105 (2013).
    • (2013) Cell Res. , vol.23 , pp. 1091-1105
    • Wan, Q.H.1
  • 12
    • 84878729685 scopus 로고    scopus 로고
    • The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
    • Wang, Z. et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat. Genet. 45, 701-706 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 701-706
    • Wang, Z.1
  • 13
    • 84889244482 scopus 로고    scopus 로고
    • Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations
    • Zhou, X. et al. Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations. Nat. Commun. 4, 2708 (2013).
    • (2013) Nat. Commun. , vol.4 , pp. 2708
    • Zhou, X.1
  • 14
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061-1067 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 15
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 Suppl 2, ii215-225 (2003).
    • (2003) Bioinformatics , vol.19 , pp. ii215-ii225
    • Stanke, M.1    Waack, S.2
  • 16
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf, I. Gene finding in novel genomes. BMC Bioinformatics 5, 59 (2004).
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 17
    • 70449379045 scopus 로고    scopus 로고
    • Genome sequence, comparative analysis, and population genetics of the domestic horse
    • Wade, C. M. et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326, 865-867 (2009).
    • (2009) Science , vol.326 , pp. 865-867
    • Wade, C.M.1
  • 18
    • 81555200041 scopus 로고    scopus 로고
    • Species-specific responses of Late Quaternary megafauna to climate and humans
    • Lorenzen, E. D. et al. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature. 479, 359-364 (2011).
    • (2011) Nature , vol.479 , pp. 359-364
    • Lorenzen, E.D.1
  • 19
    • 84879888373 scopus 로고    scopus 로고
    • Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    • Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74-78 (2013).
    • (2013) Nature , vol.499 , pp. 74-78
    • Orlando, L.1
  • 20
    • 0034077901 scopus 로고    scopus 로고
    • A compound poisson process for relaxing the molecular clock
    • Huelsenbeck, J. P., Larget, B. & Swofford, D. A compound poisson process for relaxing the molecular clock. Genetics 154, 1879-1892 (2000).
    • (2000) Genetics , vol.154 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.3
  • 21
    • 0034826388 scopus 로고    scopus 로고
    • Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores
    • Nikaido, M. et al. Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores. J. Mol. Evol. 53, 508-516 (2001).
    • (2001) J. Mol. Evol. , vol.53 , pp. 508-516
    • Nikaido, M.1
  • 22
    • 0033085003 scopus 로고    scopus 로고
    • Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework
    • Waddell, P. J., Cao, Y., Hasegawa, M. & Mindell, D. P. Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework. Syst. Biol. 48, 119-137 (1999).
    • (1999) Syst. Biol. , vol.48 , pp. 119-137
    • Waddell, P.J.1    Cao, Y.2    Hasegawa, M.3    Mindell, D.P.4
  • 23
    • 77951621301 scopus 로고    scopus 로고
    • The genome sequence of taurine cattle: A window to ruminant biology and evolution
    • Elsik, C. G. et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528 (2009).
    • (2009) Science , vol.324 , pp. 522-528
    • Elsik, C.G.1
  • 24
    • 84869003221 scopus 로고    scopus 로고
    • Analyses of pig genomes provide insight into porcine demography and evolution
    • Groenen, M. A. et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393-398 (2012).
    • (2012) Nature , vol.491 , pp. 393-398
    • Groenen, M.A.1
  • 25
    • 0141596080 scopus 로고    scopus 로고
    • The dog genome: Survey sequencing and comparative analysis
    • Kirkness, E. F. et al. The dog genome: survey sequencing and comparative analysis. Science 301, 1898-1903 (2003).
    • (2003) Science , vol.301 , pp. 1898-1903
    • Kirkness, E.F.1
  • 26
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 27
    • 34248576291 scopus 로고    scopus 로고
    • Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    • Mikkelsen, T. S. et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167-177 (2007).
    • (2007) Nature , vol.447 , pp. 167-177
    • Mikkelsen, T.S.1
  • 28
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1
  • 29
    • 2342452435 scopus 로고    scopus 로고
    • Human centromere repositioning "in progress"
    • Amor, D. J. et al. Human centromere repositioning "in progress". Proc. Natl. Acad. Sci. USA 101, 6542-6547 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 6542-6547
    • Amor, D.J.1
  • 30
    • 77649206825 scopus 로고    scopus 로고
    • Uncoupling of satellite DNA and centromeric function in the genus Equus
    • Piras, F. M. et al. Uncoupling of satellite DNA and centromeric function in the genus Equus. PLoS Genet. 6, e1000845 (2010).
    • (2010) PLoS Genet. , vol.6
    • Piras, F.M.1
  • 31
    • 34547496876 scopus 로고    scopus 로고
    • Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome
    • Villasante, A., Abad, J. P. & Mendez-Lago, M. Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome. Proc. Natl. Acad. Sci. USA 104, 10542-10547 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 10542-10547
    • Villasante, A.1    Abad, J.P.2    Mendez-Lago, M.3
  • 32
    • 4644235914 scopus 로고    scopus 로고
    • Recurrent sites for new centromere seeding
    • Ventura, M. et al. Recurrent sites for new centromere seeding. Genome Res. 14, 1696-1703 (2004).
    • (2004) Genome Res. , vol.14 , pp. 1696-1703
    • Ventura, M.1
  • 33
    • 84881593275 scopus 로고    scopus 로고
    • The nucleolus: A raft adrift in the nuclear sea or the keystone in nuclear structure?
    • O'Sullivan, J. M., Pai, D. A., Cridge, A. G., Engelke, D. R. & Ganley, A. R. The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure? Biomol. Concepts 4, 277-286 (2013).
    • (2013) Biomol. Concepts , vol.4 , pp. 277-286
    • O'Sullivan, J.M.1    Pai, D.A.2    Cridge, A.G.3    Engelke, D.R.4    Ganley, A.R.5
  • 34
    • 84874266637 scopus 로고    scopus 로고
    • Rfam 11.0: 10 Years of RNA families
    • Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic. Acids. Res. 41, D226-232 (2013).
    • (2013) Nucleic. Acids. Res. , vol.41 , pp. D226-D232
    • Burge, S.W.1
  • 35
    • 84906493054 scopus 로고    scopus 로고
    • Molecular architecture and mechanism of the anaphase-promoting complex
    • Chang, L., Zhang, Z., Yang, J., McLaughlin, S. H. & Barford, D. Molecular architecture and mechanism of the anaphase-promoting complex. Nature 513, 388-393 (2014).
    • (2014) Nature , vol.513 , pp. 388-393
    • Chang, L.1    Zhang, Z.2    Yang, J.3    McLaughlin, S.H.4    Barford, D.5
  • 36
    • 1842486792 scopus 로고    scopus 로고
    • The spindle checkpoint, aneuploidy, and cancer
    • Bharadwaj, R. & Yu, H. The spindle checkpoint, aneuploidy, and cancer. Oncogene 23, 2016-2027 (2004).
    • (2004) Oncogene , vol.23 , pp. 2016-2027
    • Bharadwaj, R.1    Yu, H.2
  • 39
    • 0842321501 scopus 로고    scopus 로고
    • MicroRNA targets in Drosophila
    • Enright, A. J. et al. MicroRNA targets in Drosophila. Genome Biol. 5, R1 (2003).
    • (2003) Genome Biol. , vol.5 , pp. R1
    • Enright, A.J.1
  • 40
    • 38049057159 scopus 로고    scopus 로고
    • MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
    • Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188-196 (2008).
    • (2008) Genome Res. , vol.18 , pp. 188-196
    • Cantarel, B.L.1
  • 41
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 42
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493-496 (2011).
    • (2011) Nature , vol.475 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 43
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J., Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 44
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 45
    • 79960403324 scopus 로고    scopus 로고
    • GenBlastG: Using BLAST searches to build homologous gene models
    • She, R. et al. genBlastG: using BLAST searches to build homologous gene models. Bioinformatics 27, 2141-2143 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2141-2143
    • She, R.1
  • 46
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic. Acids. Res. 32, 1792-1797 (2004).
    • (2004) Nucleic. Acids. Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 47
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552 (2000).
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 48
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321 (2010).
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1
  • 49
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 50
    • 33646856440 scopus 로고    scopus 로고
    • CAFE: A computational tool for the study of gene family evolution
    • De Bie, T., Cristianini, N., Demuth, J. P. & Hahn, M. W. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, 1269-1271 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 1269-1271
    • De Bie, T.1    Cristianini, N.2    Demuth, J.P.3    Hahn, M.W.4
  • 51
    • 77956193448 scopus 로고    scopus 로고
    • ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling, A. E., Mau, B. & Perna, N. T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5, e11147 (2010).
    • (2010) PLoS One , vol.5
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 52
    • 0033153375 scopus 로고    scopus 로고
    • Alignment of whole genomes
    • Delcher, A. L. et al. Alignment of whole genomes. Nucleic. Acids. Res. 27, 2369-2376 (1999).
    • (1999) Nucleic. Acids. Res. , vol.27 , pp. 2369-2376
    • Delcher, A.L.1


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