메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: A turnip, a rapid cycling and a Chinese cabbage

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC COMPOUND; PEROXIDASE; PHENYLPROPANOID; UNCLASSIFIED DRUG; GENETIC MARKER;

EID: 84902986004     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-250     Document Type: Article
Times cited : (84)

References (39)
  • 3
    • 84860424914 scopus 로고    scopus 로고
    • Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa
    • 10.1371/journal.pone.0036442, 3342247, 22567157
    • Cheng F, Wu J, Fang L, Sun S, Liu B, Lin K, Bonnema G, Wang X. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 2012, 7(5):e36442. 10.1371/journal.pone.0036442, 3342247, 22567157.
    • (2012) PLoS One , vol.7 , Issue.5
    • Cheng, F.1    Wu, J.2    Fang, L.3    Sun, S.4    Liu, B.5    Lin, K.6    Bonnema, G.7    Wang, X.8
  • 4
    • 84859564587 scopus 로고    scopus 로고
    • Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy
    • 10.1534/genetics.111.137349, 3316664, 22308264
    • Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 2012, 190(4):1563-1574. 10.1534/genetics.111.137349, 3316664, 22308264.
    • (2012) Genetics , vol.190 , Issue.4 , pp. 1563-1574
    • Tang, H.1    Woodhouse, M.R.2    Cheng, F.3    Schnable, J.C.4    Pedersen, B.S.5    Conant, G.6    Wang, X.7    Freeling, M.8    Pires, J.C.9
  • 5
    • 0001167258 scopus 로고
    • Rapid-cycling populations of brassica
    • 10.1126/science.232.4756.1385, 17828914
    • Williams PH, Hill CB. Rapid-cycling populations of brassica. Science 1986, 232(4756):1385-1389. 10.1126/science.232.4756.1385, 17828914.
    • (1986) Science , vol.232 , Issue.4756 , pp. 1385-1389
    • Williams, P.H.1    Hill, C.B.2
  • 7
    • 38049150491 scopus 로고    scopus 로고
    • A portrait of copy-number polymorphism in Drosophila melanogaster
    • 10.1073/pnas.0709888104, 2148398, 18056801
    • Dopman EB, Hartl DL. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci USA 2007, 104(50):19920-19925. 10.1073/pnas.0709888104, 2148398, 18056801.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.50 , pp. 19920-19925
    • Dopman, E.B.1    Hartl, D.L.2
  • 8
    • 78650631500 scopus 로고    scopus 로고
    • The case for resequencing studies of Arabidopsis thaliana accessions: mining the dark matter of natural genetic variation
    • Santuari L, Hardtke CS. The case for resequencing studies of Arabidopsis thaliana accessions: mining the dark matter of natural genetic variation. Biol Reprod 2010, 2:85.
    • (2010) Biol Reprod , vol.2 , pp. 85
    • Santuari, L.1    Hardtke, C.S.2
  • 10
    • 78549273825 scopus 로고    scopus 로고
    • Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
    • 10.1101/gr.109165.110, 2989995, 21036921
    • Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 2010, 20(12):1689-1699. 10.1101/gr.109165.110, 2989995, 21036921.
    • (2010) Genome Res , vol.20 , Issue.12 , pp. 1689-1699
    • Swanson-Wagner, R.A.1    Eichten, S.R.2    Kumari, S.3    Tiffin, P.4    Stein, J.C.5    Ware, D.6    Springer, N.M.7
  • 15
    • 80053914535 scopus 로고    scopus 로고
    • BRAD, the genetics and genomics database for Brassica plants
    • 10.1186/1471-2229-11-136, 3213011, 21995777
    • Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 2011, 11:136. 10.1186/1471-2229-11-136, 3213011, 21995777.
    • (2011) BMC Plant Biol , vol.11 , pp. 136
    • Cheng, F.1    Liu, S.2    Wu, J.3    Fang, L.4    Sun, S.5    Liu, B.6    Li, P.7    Hua, W.8    Wang, X.9
  • 17
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
    • 10.4161/fly.19695, 3679285, 22728672
    • Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012, 6(2):80-92. 10.4161/fly.19695, 3679285, 22728672.
    • (2012) Fly (Austin) , vol.6 , Issue.2 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    le Wang, L.3    Coon, M.4    Nguyen, T.5    Wang, L.6    Land, S.J.7    Lu, X.8    Ruden, D.M.9
  • 18
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • 3245020, 22080510
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(Database issue):D109-D114. 3245020, 22080510.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 20
    • 23644437138 scopus 로고    scopus 로고
    • Peroxidases have more functions than a Swiss army knife
    • 10.1007/s00299-005-0972-6, 15856234
    • Passardi F, Cosio C, Penel C, Dunand C. Peroxidases have more functions than a Swiss army knife. Plant Cell Rep 2005, 24(5):255-265. 10.1007/s00299-005-0972-6, 15856234.
    • (2005) Plant Cell Rep , vol.24 , Issue.5 , pp. 255-265
    • Passardi, F.1    Cosio, C.2    Penel, C.3    Dunand, C.4
  • 21
    • 80052848466 scopus 로고    scopus 로고
    • Computational methods for Gene Orthology inference
    • 10.1093/bib/bbr030, 3178053, 21690100
    • Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Computational methods for Gene Orthology inference. Brief Bioinform 2011, 12(5):379-391. 10.1093/bib/bbr030, 3178053, 21690100.
    • (2011) Brief Bioinform , vol.12 , Issue.5 , pp. 379-391
    • Kristensen, D.M.1    Wolf, Y.I.2    Mushegian, A.R.3    Koonin, E.V.4
  • 23
    • 34548555911 scopus 로고    scopus 로고
    • OMA Browser-exploring orthologous relations across 352 complete genomes
    • 10.1093/bioinformatics/btm295, 17545180
    • Schneider A, Dessimoz C, Gonnet GH. OMA Browser-exploring orthologous relations across 352 complete genomes. Bioinformatics 2007, 23(16):2180-2182. 10.1093/bioinformatics/btm295, 17545180.
    • (2007) Bioinformatics , vol.23 , Issue.16 , pp. 2180-2182
    • Schneider, A.1    Dessimoz, C.2    Gonnet, G.H.3
  • 26
    • 79953704168 scopus 로고    scopus 로고
    • The patterns of population differentiation in a Brassica rapa core collection
    • 10.1007/s00122-010-1516-1, 3057009, 21193901
    • Pino Del Carpio D, Basnet RK, De Vos RC, Maliepaard C, Visser R, Bonnema G. The patterns of population differentiation in a Brassica rapa core collection. Theor Appl Genet 2011, 122(6):1105-1118. 10.1007/s00122-010-1516-1, 3057009, 21193901.
    • (2011) Theor Appl Genet , vol.122 , Issue.6 , pp. 1105-1118
    • Pino Del Carpio, D.1    Basnet, R.K.2    De Vos, R.C.3    Maliepaard, C.4    Visser, R.5    Bonnema, G.6
  • 27
    • 21044437028 scopus 로고    scopus 로고
    • Genetic relationships within Brassica rapa as inferred from AFLP fingerprints
    • 10.1007/s00122-005-1967-y, 15806345
    • Zhao J, Wang X, Deng B, Lou P, Wu J, Sun R, Xu Z, Vromans J, Koornneef M, Bonnema G. Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor Appl Genet 2005, 110(7):1301-1314. 10.1007/s00122-005-1967-y, 15806345.
    • (2005) Theor Appl Genet , vol.110 , Issue.7 , pp. 1301-1314
    • Zhao, J.1    Wang, X.2    Deng, B.3    Lou, P.4    Wu, J.5    Sun, R.6    Xu, Z.7    Vromans, J.8    Koornneef, M.9    Bonnema, G.10
  • 28
    • 17844379449 scopus 로고    scopus 로고
    • Chromosome triplication found across the tribe Brassiceae
    • 10.1101/gr.3531105, 1074366, 15781573
    • Lysak MA, Koch MA, Pecinka A, Schubert I. Chromosome triplication found across the tribe Brassiceae. Genome Res 2005, 15(4):516-525. 10.1101/gr.3531105, 1074366, 15781573.
    • (2005) Genome Res , vol.15 , Issue.4 , pp. 516-525
    • Lysak, M.A.1    Koch, M.A.2    Pecinka, A.3    Schubert, I.4
  • 29
    • 84856246802 scopus 로고    scopus 로고
    • De novo assembly and genotyping of variants using colored de Bruijn graphs
    • 10.1038/ng.1028, 3272472, 22231483
    • Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet 2012, 44(2):226-232. 10.1038/ng.1028, 3272472, 22231483.
    • (2012) Nat Genet , vol.44 , Issue.2 , pp. 226-232
    • Iqbal, Z.1    Caccamo, M.2    Turner, I.3    Flicek, P.4    McVean, G.5
  • 30
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    • 3245008, 22121212
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012, 40(Database issue):D130-D135. 3245008, 22121212.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 31
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • 10.1186/1471-2105-5-59, 421630, 15144565
    • Korf I. Gene finding in novel genomes. BMC Bioinformatics 2004, 5:59. 10.1186/1471-2105-5-59, 421630, 15144565.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 32
    • 29144453390 scopus 로고    scopus 로고
    • Gene identification in novel eukaryotic genomes by self-training algorithm
    • 10.1093/nar/gki937, 1298918, 16314312
    • Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 2005, 33(20):6494-6506. 10.1093/nar/gki937, 1298918, 16314312.
    • (2005) Nucleic Acids Res , vol.33 , Issue.20 , pp. 6494-6506
    • Lomsadze, A.1    Ter-Hovhannisyan, V.2    Chernoff, Y.O.3    Borodovsky, M.4
  • 33
    • 33748674197 scopus 로고    scopus 로고
    • AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
    • 10.1186/gb-2006-7-s1-s11, 1810548, 16925833
    • Stanke M, Tzvetkova A, Morgenstern B. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol 2006, 7(Suppl 1):S11-S18. 10.1186/gb-2006-7-s1-s11, 1810548, 16925833.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL 1
    • Stanke, M.1    Tzvetkova, A.2    Morgenstern, B.3
  • 34
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 35
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: tools for protein sequence classification and comparison
    • 10.1007/978-1-59745-515-2_5, 18025686
    • Mulder N, Apweiler R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 2007, 396:59-70. 10.1007/978-1-59745-515-2_5, 18025686.
    • (2007) Methods Mol Biol , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 36
    • 43949138227 scopus 로고    scopus 로고
    • Blast2GO: A comprehensive suite for functional analysis in plant genomics
    • 2375974, 18483572
    • Conesa A, Gotz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008, 2008:619832. 2375974, 18483572.
    • (2008) Int J Plant Genomics , vol.2008 , pp. 619832
    • Conesa, A.1    Gotz, S.2
  • 37
    • 38549122308 scopus 로고    scopus 로고
    • InParanoid 6: eukaryotic ortholog clusters with inparalogs
    • 2238924, 18055500
    • Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL. InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res 2008, 36(Database issue):D263-D266. 2238924, 18055500.
    • (2008) Nucleic Acids Res , vol.36 , Issue.DATABASE ISSUE
    • Berglund, A.C.1    Sjolund, E.2    Ostlund, G.3    Sonnhammer, E.L.4
  • 38
    • 0036513591 scopus 로고    scopus 로고
    • EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite
    • 10.1093/bib/3.1.87, 12002227
    • Olson SA. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 2002, 3(1):87-91. 10.1093/bib/3.1.87, 12002227.
    • (2002) Brief Bioinform , vol.3 , Issue.1 , pp. 87-91
    • Olson, S.A.1
  • 39
    • 84864530626 scopus 로고    scopus 로고
    • Bayesian Phylogenetics with BEAUti and the BEAST 1.7
    • 10.1093/molbev/mss075, 3408070, 22367748
    • Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012, 29(8):1969-1973. 10.1093/molbev/mss075, 3408070, 22367748.
    • (2012) Mol Biol Evol , vol.29 , Issue.8 , pp. 1969-1973
    • Drummond, A.J.1    Suchard, M.A.2    Xie, D.3    Rambaut, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.