메뉴 건너뛰기




Volumn 44, Issue 1, 2017, Pages 51-61

Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes

Author keywords

Aegilops tauschii; Comparative genomics; Genome sequencing; Grass evolution; Sequence assembly

Indexed keywords

AEGILOPS TAUSCHII; ARTICLE; BRACHYPODIUM; CHROMOSOME ARM; COMPARATIVE STUDY; GENE NUMBER; GENE SEQUENCE; GENETIC RECOMBINATION; INTERSPECIFIC HYBRIDIZATION; MOLECULAR EVOLUTION; MOLECULAR SIZE; NEXT GENERATION SEQUENCING; NONHUMAN; PLANT CHROMOSOME; PLANT GENOME; POLYPLOIDY; RICE; SEQUENCE ANALYSIS; SORGHUM; SYNTENY; TRANSPOSON; WHEAT; GENETICS; INDEL MUTATION; POACEAE; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 85005916196     PISSN: 16738527     EISSN: 18735533     Source Type: Journal    
DOI: 10.1016/j.jgg.2016.09.005     Document Type: Article
Times cited : (11)

References (65)
  • 3
    • 84936817891 scopus 로고    scopus 로고
    • Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum)
    • Akpinar, B.A., Lucas, S.J., Vrana, J., Dolezel, J., Budak, H., Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum). Plant Biotechnol. J. 13 (2015), 740–752.
    • (2015) Plant Biotechnol. J. , vol.13 , pp. 740-752
    • Akpinar, B.A.1    Lucas, S.J.2    Vrana, J.3    Dolezel, J.4    Budak, H.5
  • 4
    • 51649150815 scopus 로고
    • Nuclear DNA content of some important plant species
    • Arumuganathan, K., Earle, E.D., Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9 (1991), 208–218.
    • (1991) Plant Mol. Biol. Rep. , vol.9 , pp. 208-218
    • Arumuganathan, K.1    Earle, E.D.2
  • 9
    • 34347399464 scopus 로고    scopus 로고
    • Genome plasticity a key factor in the success of polyploid wheat under domestication
    • Dubcovsky, J., Dvorak, J., Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316 (2007), 1862–1866.
    • (2007) Science , vol.316 , pp. 1862-1866
    • Dubcovsky, J.1    Dvorak, J.2
  • 10
    • 26444545621 scopus 로고    scopus 로고
    • Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance
    • Dvorak, J., Akhunov, E.D., Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance. Genetics 171 (2005), 323–332.
    • (2005) Genetics , vol.171 , pp. 323-332
    • Dvorak, J.1    Akhunov, E.D.2
  • 12
    • 2642610283 scopus 로고    scopus 로고
    • Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species
    • Dvorak, J., Luo, M.C., Yang, Z.L., Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species. Genetics 148 (1998), 423–434.
    • (1998) Genetics , vol.148 , pp. 423-434
    • Dvorak, J.1    Luo, M.C.2    Yang, Z.L.3
  • 13
    • 0013069107 scopus 로고
    • Inferred chromosome morphology of the ancestral genome of Triticum
    • Dvorak, J., Mcguire, P.E., Mendlinger, S., Inferred chromosome morphology of the ancestral genome of Triticum. Plant Syst. Evol. 144 (1984), 209–220.
    • (1984) Plant Syst. Evol. , vol.144 , pp. 209-220
    • Dvorak, J.1    Mcguire, P.E.2    Mendlinger, S.3
  • 14
    • 0027272045 scopus 로고
    • The evolution of polyploid wheats: identification of the A genome donor species
    • Dvorak, J., Terlizzi, P., Zhang, H.B., Resta, P., The evolution of polyploid wheats: identification of the A genome donor species. Genome 36 (1993), 21–31.
    • (1993) Genome , vol.36 , pp. 21-31
    • Dvorak, J.1    Terlizzi, P.2    Zhang, H.B.3    Resta, P.4
  • 15
    • 10844286382 scopus 로고    scopus 로고
    • Deletion polymorphism in wheat chromosome regions with contrasting recombination rates
    • Dvorak, J., Yang, Z.L., You, F.M., Luo, M.C., Deletion polymorphism in wheat chromosome regions with contrasting recombination rates. Genetics 168 (2004), 1665–1675.
    • (2004) Genetics , vol.168 , pp. 1665-1675
    • Dvorak, J.1    Yang, Z.L.2    You, F.M.3    Luo, M.C.4
  • 16
    • 0025632914 scopus 로고
    • Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes
    • Dvorak, J., Zhang, H.B., Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc. Natl. Acad. Sci. U. S. A. 87 (1990), 9640–9644.
    • (1990) Proc. Natl. Acad. Sci. U. S. A. , vol.87 , pp. 9640-9644
    • Dvorak, J.1    Zhang, H.B.2
  • 18
    • 70349288278 scopus 로고    scopus 로고
    • Genome evolution in allopolyploid wheat-a revolutionary reprogramming followed by gradual changes
    • Feldman, M., Levy, A.A., Genome evolution in allopolyploid wheat-a revolutionary reprogramming followed by gradual changes. J. Genet. Genomics 36 (2009), 511–518.
    • (2009) J. Genet. Genomics , vol.36 , pp. 511-518
    • Feldman, M.1    Levy, A.A.2
  • 19
    • 84941141643 scopus 로고    scopus 로고
    • Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B
    • Glover, N.M., Daron, J., Pingault, L., Vandepoele, K., Paux, E., Feuillet, C., Choulet, F., Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. Genome Biol., 16, 2015, 188.
    • (2015) Genome Biol. , vol.16 , pp. 188
    • Glover, N.M.1    Daron, J.2    Pingault, L.3    Vandepoele, K.4    Paux, E.5    Feuillet, C.6    Choulet, F.7
  • 20
    • 84890011303 scopus 로고    scopus 로고
    • Consed: a graphical editor for next-generation sequencing
    • Gordon, D., Green, P., Consed: a graphical editor for next-generation sequencing. Bioinformatics 29 (2013), 2936–2937.
    • (2013) Bioinformatics , vol.29 , pp. 2936-2937
    • Gordon, D.1    Green, P.2
  • 23
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the model grass Brachypodium distachyon
    • International Brachypodium Initiative, Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463 (2010), 763–768.
    • (2010) Nature , vol.463 , pp. 763-768
    • International Brachypodium Initiative1
  • 24
  • 25
    • 84904382612 scopus 로고    scopus 로고
    • A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
    • International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 345, 2014, 1251788.
    • (2014) Science , vol.345 , pp. 1251788
  • 28
    • 0001018539 scopus 로고
    • Discovery of the DD-analyser, one of the ancestors of Triticum vulgare
    • Kihara, H., Discovery of the DD-analyser, one of the ancestors of Triticum vulgare. Agri. Hort. 19 (1944), 13–14.
    • (1944) Agri. Hort. , vol.19 , pp. 13-14
    • Kihara, H.1
  • 31
    • 1542338594 scopus 로고    scopus 로고
    • Genomic duplication, fractionation and the origin of regulatory novelty
    • Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A., Freeling, M., Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166 (2004), 935–945.
    • (2004) Genetics , vol.166 , pp. 935-945
    • Langham, R.J.1    Walsh, J.2    Dunn, M.3    Ko, C.4    Goff, S.A.5    Freeling, M.6
  • 34
    • 84903618373 scopus 로고    scopus 로고
    • mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat
    • Li, A., Liu, D., Wu, J., Zhao, X., Hao, M., Geng, S., Yan, J., Jiang, X., Zhang, L., Wu, J., Yin, L., Zhang, R., Wu, L., Zheng, Y., Mao, L., mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. Plant Cell 26 (2014), 1878–1900.
    • (2014) Plant Cell , vol.26 , pp. 1878-1900
    • Li, A.1    Liu, D.2    Wu, J.3    Zhao, X.4    Hao, M.5    Geng, S.6    Yan, J.7    Jiang, X.8    Zhang, L.9    Wu, J.10    Yin, L.11    Zhang, R.12    Wu, L.13    Zheng, Y.14    Mao, L.15
  • 35
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li, H., Durbin, R., Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26 (2010), 589–595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 37
    • 0000764225 scopus 로고
    • Conspectus of the Triticeae
    • Love, A., Conspectus of the Triticeae. Feddes Repert. 95 (1984), 425–521.
    • (1984) Feddes Repert. , vol.95 , pp. 425-521
    • Love, A.1
  • 43
    • 77957217584 scopus 로고
    • The origin of Triticum spelta and its free-threshing hexaploid relatives
    • Mc, F.E., Sears, E.R., The origin of Triticum spelta and its free-threshing hexaploid relatives. J. Hered. 37 (1946), 107–116.
    • (1946) J. Hered. , vol.37 , pp. 107-116
    • Mc, F.E.1    Sears, E.R.2
  • 45
    • 0001801997 scopus 로고    scopus 로고
    • From stable crop to extinction? The archaeology and history of the hulled wheats
    • S. Padulosi K.,J.,H. Hammer International Plant Genetic Resources Institute Rome
    • Nesbitt, M., Samuels, D.C., From stable crop to extinction? The archaeology and history of the hulled wheats. Padulosi, S., Hammer, K.,J.,H., (eds.) Hulled Wheats, 1996, International Plant Genetic Resources Institute, Rome, 41–100.
    • (1996) Hulled Wheats , pp. 41-100
    • Nesbitt, M.1    Samuels, D.C.2
  • 47
    • 0003515251 scopus 로고
    • Evolution by Gene Duplication
    • Springer Berlin Heidelberg
    • Ohno, S., Evolution by Gene Duplication. 1970, Springer, Berlin Heidelberg.
    • (1970)
    • Ohno, S.1
  • 48
    • 84893978887 scopus 로고    scopus 로고
    • The origin of unusual chromosome constitutions among newly formed allopolyploids
    • Oleszczuk, S., Lukaszewski, A.J., The origin of unusual chromosome constitutions among newly formed allopolyploids. Am. J. Bot. 101 (2014), 318–326.
    • (2014) Am. J. Bot. , vol.101 , pp. 318-326
    • Oleszczuk, S.1    Lukaszewski, A.J.2
  • 50
    • 0038550526 scopus 로고
    • Nuclear DNA and evolution of wheat
    • Rees, H., Walters, M.R., Nuclear DNA and evolution of wheat. Heredity 20 (1965), 73–82.
    • (1965) Heredity , vol.20 , pp. 73-82
    • Rees, H.1    Walters, M.R.2
  • 52
    • 84937699889 scopus 로고    scopus 로고
    • RepeatMasker Open-4.0
    • Smit, A., Hubley, R., Green, P., RepeatMasker Open-4.0. 2015 http://www.repeatmasker.org/.
    • (2015)
    • Smit, A.1    Hubley, R.2    Green, P.3
  • 55
    • 84876413103 scopus 로고    scopus 로고
    • Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat
    • Wang, J., Luo, M.C., Chen, Z., You, F.M., Wei, Y., Zheng, Y., Dvorak, J., Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. New Phytol. 198 (2013), 925–937.
    • (2013) New Phytol. , vol.198 , pp. 925-937
    • Wang, J.1    Luo, M.C.2    Chen, Z.3    You, F.M.4    Wei, Y.5    Zheng, Y.6    Dvorak, J.7
  • 59
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu, T.D., Nacu, S., Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26 (2010), 873–881.
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 60
    • 84874710448 scopus 로고    scopus 로고
    • gKaKs: the pipeline for genome-level Ka/Ks calculation
    • Zhang, C., Wang, J., Long, M., Fan, C., gKaKs: the pipeline for genome-level Ka/Ks calculation. Bioinformatics 29 (2013), 645–646.
    • (2013) Bioinformatics , vol.29 , pp. 645-646
    • Zhang, C.1    Wang, J.2    Long, M.3    Fan, C.4
  • 62
    • 84864867560 scopus 로고    scopus 로고
    • Total centromere size and genome size are strongly correlated in ten grass species
    • Zhang, H., Dawe, R.K., Total centromere size and genome size are strongly correlated in ten grass species. Chromosome Res. 20 (2012), 403–412.
    • (2012) Chromosome Res. , vol.20 , pp. 403-412
    • Zhang, H.1    Dawe, R.K.2
  • 63
    • 84995466960 scopus 로고    scopus 로고
    • Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences
    • Zhang, J., Kudrna, D., Mu, T., Li, W., Copetti, D., Yu, Y., Goicoechea, J.L., Lei, Y., Wing, R.A., Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics 32 (2016), 3058–3064.
    • (2016) Bioinformatics , vol.32 , pp. 3058-3064
    • Zhang, J.1    Kudrna, D.2    Mu, T.3    Li, W.4    Copetti, D.5    Yu, Y.6    Goicoechea, J.L.7    Lei, Y.8    Wing, R.A.9
  • 65
    • 79960125436 scopus 로고    scopus 로고
    • Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat
    • Zhao, N., Zhu, B., Li, M., Wang, L., Xu, L., Zhang, H., Zheng, S., Qi, B., Han, F., Liu, B., Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat. Genetics 188 (2011), 499–510.
    • (2011) Genetics , vol.188 , pp. 499-510
    • Zhao, N.1    Zhu, B.2    Li, M.3    Wang, L.4    Xu, L.5    Zhang, H.6    Zheng, S.7    Qi, B.8    Han, F.9    Liu, B.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.