메뉴 건너뛰기




Volumn 168, Issue 4, 2015, Pages 1433-1447

A comparative epigenomic analysis of polyploidy-derived genes in soybean and common bean

Author keywords

[No Author keywords available]

Indexed keywords

GLYCINE MAX; PHASEOLUS VULGARIS;

EID: 84939139239     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.15.00408     Document Type: Article
Times cited : (81)

References (85)
  • 1
    • 79961001437 scopus 로고    scopus 로고
    • Genomewide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis
    • Ahmed I, Sarazin A, Bowler C, Colot V, Quesneville H (2011) Genomewide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res 39: 6919- 6931
    • (2011) Nucleic Acids Res , vol.39 , pp. 6919-6931
    • Ahmed, I.1    Sarazin, A.2    Bowler, C.3    Colot, V.4    Quesneville, H.5
  • 4
    • 0019322245 scopus 로고
    • DNA methylation and the frequency of CpG in animal DNA
    • Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8: 1499-1504
    • (1980) Nucleic Acids Res , vol.8 , pp. 1499-1504
    • Bird, A.P.1
  • 5
    • 0037468758 scopus 로고    scopus 로고
    • Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    • Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438
    • (2003) Nature , vol.422 , pp. 433-438
    • Bowers, J.E.1    Chapman, B.A.2    Rong, J.3    Paterson, A.H.4
  • 6
    • 84899651940 scopus 로고    scopus 로고
    • Enhanced evolution by stochastically variable modification of epigenetic marks in the early embryo
    • Branciamore S, Rodin AS, Riggs AD, Rodin SN (2014) Enhanced evolution by stochastically variable modification of epigenetic marks in the early embryo. Proc Natl Acad Sci USA 111: 6353-6358
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 6353-6358
    • Branciamore, S.1    Rodin, A.S.2    Riggs, A.D.3    Rodin, S.N.4
  • 7
    • 0015189585 scopus 로고
    • Control of leghaemoglobin synthesis in snake beans
    • Broughton WJ, Dilworth MJ (1971) Control of leghaemoglobin synthesis in snake beans. Biochem J 125: 1075-1080
    • (1971) Biochem J , vol.125 , pp. 1075-1080
    • Broughton, W.J.1    Dilworth, M.J.2
  • 10
    • 84868122260 scopus 로고    scopus 로고
    • Deposition of histone variant H2A.Z within gene bodies regulates responsive genes
    • Coleman-Derr D, Zilberman D (2012) Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet 8: e1002988
    • (2012) PLoS Genet , vol.8
    • Coleman-Derr, D.1    Zilberman, D.2
  • 14
  • 15
    • 84857757793 scopus 로고    scopus 로고
    • Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean
    • Du J, Tian Z, Sui Y, Zhao M, Song Q, Cannon SB, Cregan P, Ma J (2012) Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean. Plant Cell 24: 21-32
    • (2012) Plant Cell , vol.24 , pp. 21-32
    • Du, J.1    Tian, Z.2    Sui, Y.3    Zhao, M.4    Song, Q.5    Cannon, S.B.6    Cregan, P.7    Ma, J.8
  • 16
    • 77954299992 scopus 로고    scopus 로고
    • agriGO: A GO analysis toolkit for the agricultural community
    • Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010b) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-W70
    • (2010) Nucleic Acids Res , vol.38 , pp. W64-W70
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 17
    • 77950191132 scopus 로고    scopus 로고
    • Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels
    • Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens- Mack J, dePamphilis CW (2010) Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol 10: 61
    • (2010) BMC Evol Biol , vol.10 , pp. 61
    • Duarte, J.M.1    Wall, P.K.2    Edger, P.P.3    Landherr, L.L.4    Ma, H.5    Pires, J.C.6    Leebens-Mack, J.7    dePamphilis, C.W.8
  • 22
    • 67651039811 scopus 로고    scopus 로고
    • Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition
    • Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol 60: 433-453
    • (2009) Annu Rev Plant Biol , vol.60 , pp. 433-453
    • Freeling, M.1
  • 25
    • 43249115146 scopus 로고    scopus 로고
    • Testing the ratio of two Poisson rates
    • Gu K, Ng HK, Tang ML, Schucany WR (2008) Testing the ratio of two Poisson rates. Biom J 50: 283-298
    • (2008) Biom J , vol.50 , pp. 283-298
    • Gu, K.1    Ng, H.K.2    Tang, M.L.3    Schucany, W.R.4
  • 26
    • 12344335569 scopus 로고    scopus 로고
    • DAGchainer: A tool for mining segmental genome duplications and synteny
    • Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643-3646
    • (2004) Bioinformatics , vol.20 , pp. 3643-3646
    • Haas, B.J.1    Delcher, A.L.2    Wortman, J.R.3    Salzberg, S.L.4
  • 27
    • 0003079258 scopus 로고
    • Speciation and cytogenetics
    • BE Caldwell, ed, American Society of Agronomy, Madison, WI
    • Hadley HH, Hymowitz T (1973) Speciation and cytogenetics. In BE Caldwell, ed, Soybeans: Improvement, Production, and Uses. American Society of Agronomy, Madison, WI, pp 96-116
    • (1973) Soybeans: Improvement, Production, and Uses , pp. 96-116
    • Hadley, H.H.1    Hymowitz, T.2
  • 28
    • 75549087305 scopus 로고    scopus 로고
    • The evolution of gene duplications: Classifying and distinguishing between models
    • Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11: 97-108
    • (2010) Nat Rev Genet , vol.11 , pp. 97-108
    • Innan, H.1    Kondrashov, F.2
  • 29
    • 84875732837 scopus 로고    scopus 로고
    • Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants
    • Jiang WK, Liu YL, Xia EH, Gao LZ (2013) Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. Plant Physiol 161: 1844-1861
    • (2013) Plant Physiol , vol.161 , pp. 1844-1861
    • Jiang, W.K.1    Liu, Y.L.2    Xia, E.H.3    Gao, L.Z.4
  • 31
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36
    • (2013) Genome Biol , vol.14
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 32
    • 70350655959 scopus 로고    scopus 로고
    • Dynamic rearrangements determine genome organization and useful traits in soybean
    • Kim KD, Shin JH, Van K, Kim DH, Lee SH (2009) Dynamic rearrangements determine genome organization and useful traits in soybean. Plant Physiol 151: 1066-1076
    • (2009) Plant Physiol , vol.151 , pp. 1066-1076
    • Kim, K.D.1    Shin, J.H.2    Van, K.3    Kim, D.H.4    Lee, S.H.5
  • 33
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571-1572
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 34
    • 0001515552 scopus 로고
    • Chromosome numbers in the Phaseoleae (Fabaceae: Faboideae) and their relation to taxonomy
    • Lackey JA (1980) Chromosome numbers in the Phaseoleae (Fabaceae: Faboideae) and their relation to taxonomy. Am J Bot 67: 595-602
    • (1980) Am J Bot , vol.67 , pp. 595-602
    • Lackey, J.A.1
  • 35
    • 25144446148 scopus 로고    scopus 로고
    • Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary
    • Lavin M, Herendeen PS, Wojciechowski MF (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol 54: 575-594
    • (2005) Syst Biol , vol.54 , pp. 575-594
    • Lavin, M.1    Herendeen, P.S.2    Wojciechowski, M.F.3
  • 36
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220
    • (2010) Nat Rev Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 38
    • 84863103782 scopus 로고    scopus 로고
    • Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
    • Li X, Zhu J, Hu F, Ge S, Ye M, Xiang H, Zhang G, Zheng X, Zhang H, Zhang S, et al (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics 13: 300
    • (2012) BMC Genomics , vol.13 , pp. 300
    • Li, X.1    Zhu, J.2    Hu, F.3    Ge, S.4    Ye, M.5    Xiang, H.6    Zhang, G.7    Zheng, X.8    Zhang, H.9    Zhang, S.10
  • 40
    • 66449124318 scopus 로고    scopus 로고
    • Epigenetic regulation of transposable elements in plants
    • Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60: 43-66
    • (2009) Annu Rev Plant Biol , vol.60 , pp. 43-66
    • Lisch, D.1
  • 43
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 45
    • 84881177437 scopus 로고    scopus 로고
    • Genetic and epigenetic aspects of polyploid evolution in plants
    • Madlung A, Wendel JF (2013) Genetic and epigenetic aspects of polyploid evolution in plants. Cytogenet Genome Res 140: 270-285
    • (2013) Cytogenet Genome Res , vol.140 , pp. 270-285
    • Madlung, A.1    Wendel, J.F.2
  • 46
    • 84902365207 scopus 로고    scopus 로고
    • Transposable elements, a treasure trove to decipher epigenetic variation: Insights from Arabidopsis and crop epigenomes
    • Mirouze M, Vitte C (2014) Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. J Exp Bot 65: 2801-2812
    • (2014) J Exp Bot , vol.65 , pp. 2801-2812
    • Mirouze, M.1    Vitte, C.2
  • 48
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • Papp B, Pál C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197
    • (2003) Nature , vol.424 , pp. 194-197
    • Papp, B.1    Pál, C.2    Hurst, L.D.3
  • 50
    • 84856468953 scopus 로고    scopus 로고
    • NGS QC Toolkit: A toolkit for quality control of next generation sequencing data
    • Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7: e30619
    • (2012) PLoS ONE , vol.7
    • Patel, R.K.1    Jain, M.2
  • 51
    • 33750173564 scopus 로고    scopus 로고
    • Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
    • Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC (2006) Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 22: 597-602
    • (2006) Trends Genet , vol.22 , pp. 597-602
    • Paterson, A.H.1    Chapman, B.A.2    Kissinger, J.C.3    Bowers, J.E.4    Feltus, F.A.5    Estill, J.C.6
  • 53
    • 84887015270 scopus 로고    scopus 로고
    • Hidden genetic nature of epigenetic natural variation in plants
    • Pecinka A, Abdelsamad A, Vu GT (2013) Hidden genetic nature of epigenetic natural variation in plants. Trends Plant Sci 18: 625-632
    • (2013) Trends Plant Sci , vol.18 , pp. 625-632
    • Pecinka, A.1    Abdelsamad, A.2    Vu, G.T.3
  • 54
    • 84900844522 scopus 로고    scopus 로고
    • Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology
    • Qiao Z, Libault M (2013) Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology. Front Plant Sci 4: 484
    • (2013) Front Plant Sci , vol.4 , pp. 484
    • Qiao, Z.1    Libault, M.2
  • 55
    • 0038031633 scopus 로고    scopus 로고
    • Epigenetic silencing may aid evolution by gene duplication
    • Rodin SN, Riggs AD (2003) Epigenetic silencing may aid evolution by gene duplication. J Mol Evol 56: 718-729
    • (2003) J Mol Evol , vol.56 , pp. 718-729
    • Rodin, S.N.1    Riggs, A.D.2
  • 61
    • 4444363053 scopus 로고    scopus 로고
    • Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
    • Seoighe C, Gehring C (2004) Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet 20: 461- 464
    • (2004) Trends Genet , vol.20 , pp. 461-464
    • Seoighe, C.1    Gehring, C.2
  • 62
    • 0032879798 scopus 로고    scopus 로고
    • Yeast genome evolution in the post-genome era
    • Seoighe C, Wolfe KH (1999) Yeast genome evolution in the post-genome era. Curr Opin Microbiol 2: 548-554
    • (1999) Curr Opin Microbiol , vol.2 , pp. 548-554
    • Seoighe, C.1    Wolfe, K.H.2
  • 63
    • 84912120604 scopus 로고    scopus 로고
    • Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization
    • Seymour DK, Koenig D, Hagmann J, Becker C, Weigel D (2014) Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet 10: e1004785
    • (2014) PLoS Genet , vol.10
    • Seymour, D.K.1    Koenig, D.2    Hagmann, J.3    Becker, C.4    Weigel, D.5
  • 67
    • 84872614860 scopus 로고    scopus 로고
    • Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome
    • Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152: 352-364
    • (2013) Cell , vol.152 , pp. 352-364
    • Stroud, H.1    Greenberg, M.V.2    Feng, S.3    Bernatavichute, Y.V.4    Jacobsen, S.E.5
  • 68
    • 84861062626 scopus 로고    scopus 로고
    • Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly
    • Takuno S, Gaut BS (2012) Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol 29: 219-227
    • (2012) Mol Biol Evol , vol.29 , pp. 219-227
    • Takuno, S.1    Gaut, B.S.2
  • 69
    • 84873156452 scopus 로고    scopus 로고
    • Gene body methylation is conserved between plant orthologs and is of evolutionary consequence
    • Takuno S, Gaut BS (2013) Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci USA 110: 1797-1802
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 1797-1802
    • Takuno, S.1    Gaut, B.S.2
  • 70
    • 77955273950 scopus 로고    scopus 로고
    • A triptych of the evolution of plant transposable elements
    • Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15: 471-478
    • (2010) Trends Plant Sci , vol.15 , pp. 471-478
    • Tenaillon, M.I.1    Hollister, J.D.2    Gaut, B.S.3
  • 71
    • 33745617700 scopus 로고    scopus 로고
    • Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
    • Thomas BC, Pedersen B, Freeling M (2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 16: 934-946
    • (2006) Genome Res , vol.16 , pp. 934-946
    • Thomas, B.C.1    Pedersen, B.2    Freeling, M.3
  • 73
    • 84905647470 scopus 로고    scopus 로고
    • Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary
    • Vanneste K, Baele G, Maere S, Van de Peer Y (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res 24: 1334-1347
    • (2014) Genome Res , vol.24 , pp. 1334-1347
    • Vanneste, K.1    Baele, G.2    Maere, S.3    Van de Peer, Y.4
  • 75
    • 84866940769 scopus 로고    scopus 로고
    • Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica)
    • Vonholdt BM, Takuno S, Gaut BS (2012) Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol 29: 3193-3203
    • (2012) Mol Biol Evol , vol.29 , pp. 3193-3203
    • Vonholdt, B.M.1    Takuno, S.2    Gaut, B.S.3
  • 77
    • 84874196086 scopus 로고    scopus 로고
    • Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice)
    • Wang Y, Wang X, Lee TH, Mansoor S, Paterson AH (2013) Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice). New Phytol 198: 274-283
    • (2013) New Phytol , vol.198 , pp. 274-283
    • Wang, Y.1    Wang, X.2    Lee, T.H.3    Mansoor, S.4    Paterson, A.H.5
  • 78
    • 0035344021 scopus 로고    scopus 로고
    • Yesterday's polyploids and the mystery of diploidization
    • Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2: 333-341
    • (2001) Nat Rev Genet , vol.2 , pp. 333-341
    • Wolfe, K.H.1
  • 79
    • 79961064486 scopus 로고    scopus 로고
    • Factors that contribute to variation in evolutionary rate among Arabidopsis genes
    • Yang L, Gaut BS (2011) Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol 28: 2359-2369
    • (2011) Mol Biol Evol , vol.28 , pp. 2359-2369
    • Yang, L.1    Gaut, B.S.2
  • 81
    • 77952355762 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation
    • Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-919
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1    McDaniel, I.E.2    Silva, P.3    Zilberman, D.4
  • 82
    • 53449101955 scopus 로고    scopus 로고
    • Genome duplication and the origin of the vertebrate skeleton
    • Zhang G, Cohn MJ (2008) Genome duplication and the origin of the vertebrate skeleton. Curr Opin Genet Dev 18: 387-393
    • (2008) Curr Opin Genet Dev , vol.18 , pp. 387-393
    • Zhang, G.1    Cohn, M.J.2
  • 83
    • 57149109127 scopus 로고    scopus 로고
    • DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya
    • Zhang W, Wang X, Yu Q, Ming R, Jiang J (2008) DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res 18: 1938-1943
    • (2008) Genome Res , vol.18 , pp. 1938-1943
    • Zhang, W.1    Wang, X.2    Yu, Q.3    Ming, R.4    Jiang, J.5
  • 85
    • 33845880624 scopus 로고    scopus 로고
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69
    • (2007) Nat Genet , vol.39 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.