메뉴 건너뛰기




Volumn 4, Issue 11, 2014, Pages 2065-2078

Polymorphism identification and improved genome annotation of Brassica rapa through deep RNA sequencing

Author keywords

Annotation; Brassica rapa; Genome; RNA Seq; SNPs; Transcriptome

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

EID: 84910642171     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.012526     Document Type: Article
Times cited : (28)

References (45)
  • 2
    • 37249005195 scopus 로고    scopus 로고
    • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    • Brent, M. R., 2008 Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat. Rev. Genet. 9: 62-73.
    • (2008) Nat. Rev. Genet , vol.9 , pp. 62-73
    • Brent, M.R.1
  • 3
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C., and S. Karlin, 1997 Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
    • (1997) J. Mol. Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 4
    • 84879482267 scopus 로고    scopus 로고
    • Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa.
    • Cheng, F., T. Mandakova, J. Wu, Q. Xie, M. A. Lysak et al., 2013 Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. Plant Cell 25: 1541-1554.
    • (2013) Plant Cell , vol.25 , pp. 1541-1554
    • Cheng, F.1    Mandakova, T.2    Wu, J.3    Xie, Q.4    Lysak, M.A.5
  • 5
    • 84860424914 scopus 로고    scopus 로고
    • Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa.
    • Cheng, F., J. Wu, L. Fang, S. Sun, B. Liu et al., 2012 Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS ONE 7: e36442.
    • (2012) PLoS ONE , vol.7
    • Cheng, F.1    Wu, J.2    Fang, L.3    Sun, S.4    Liu, B.5
  • 6
    • 0038744804 scopus 로고    scopus 로고
    • SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
    • Ching, A., K. S. Caldwell, M. Jung, M. Dolan, O. S. Smith et al., 2002 SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. 3: 19.
    • (2002) BMC Genet , vol.3 , pp. 19
    • Ching, A.1    Caldwell, K.S.2    Jung, M.3    Dolan, M.4    Smith, O.S.5
  • 7
    • 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.
    • (Austin)
    • Cingolani, P., and A. Platts, L. Wang le, M. Coon, T. Nguyen et al., 2012 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) 6: 80-92.
    • (2012) Fly , vol.6 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    Wang Le, L.3    Coon, M.4    Nguyen, T.5
  • 8
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
    • Conesa, A., S. Gotz, J. M. Garcia-Gomez, J. Terol, M. Talon et al., 2005 Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5
  • 11
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using nextgeneration DNA sequencing data
    • DePristo, M. A., E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire et al., 2011 A framework for variation discovery and genotyping using nextgeneration DNA sequencing data. Nat. Genet. 43: 491-498.
    • (2011) Nat. Genet , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4    Maguire, J.R.5
  • 12
    • 0026080330 scopus 로고
    • Genetics of Brassica campestris. 1. Genetic constraints on evolution of life-history characters.
    • Dorn, L. A., and T. Mitchell-Olds, 1991 Genetics of Brassica campestris. 1. Genetic constraints on evolution of life-history characters. Evolution 45: 371-379.
    • (1991) Evolution , vol.45 , pp. 371-379
    • Dorn, L.A.1    Mitchell-Olds, T.2
  • 13
    • 79953096336 scopus 로고    scopus 로고
    • The quantitative-genetic and QTL architecture of trait integration and modularity in Brassica rapa across simulated seasonal settings.
    • Edwards, C. E., and C. Weinig, 2011 The quantitative-genetic and QTL architecture of trait integration and modularity in Brassica rapa across simulated seasonal settings. Heredity 106: 661-677.
    • (2011) Heredity , vol.106 , pp. 661-677
    • Edwards, C.E.1    Weinig, C.2
  • 14
    • 70349678826 scopus 로고    scopus 로고
    • Genotypes of Brassica rapa respond differently to plant-induced variation in air CO2 concentration in growth chambers with standard and enhanced venting
    • Edwards, C. E., M. S. Haselhorst, A. M. McKnite, B. E. Ewers, D. G. Williams et al., 2009 Genotypes of Brassica rapa respond differently to plant-induced variation in air CO2 concentration in growth chambers with standard and enhanced venting. Theor. Appl. Genet. 119: 991-1004.
    • (2009) Theor. Appl. Genet , vol.119 , pp. 991-1004
    • Edwards, C.E.1    Haselhorst, M.S.2    McKnite, A.M.3    Ewers, B.E.4    Williams, D.G.5
  • 15
    • 1942502343 scopus 로고    scopus 로고
    • Plant bioinformatics: from genome to phenome
    • Edwards, D., and J. Batley, 2004 Plant bioinformatics: from genome to phenome. Trends Biotechnol. 22: 232-237.
    • (2004) Trends Biotechnol , vol.22 , pp. 232-237
    • Edwards, D.1    Batley, J.2
  • 16
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq.
    • Garber, M., M. G. Grabherr, M. Guttman, and C. Trapnell, 2011 Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8: 469-477.
    • (2011) Nat. Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 17
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M. G., B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29: 644-652.
    • (2011) Nat. Biotechnol , vol.29 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3    Levin, J.Z.4    Thompson, D.A.5
  • 18
    • 77952231080 scopus 로고    scopus 로고
    • Advancing RNA-Seq analysis
    • Haas, B. J., and M. C. Zody, 2010 Advancing RNA-Seq analysis. Nat. Biotechnol. 28: 421-423.
    • (2010) Nat. Biotechnol , vol.28 , pp. 421-423
    • Haas, B.J.1    Zody, M.C.2
  • 19
    • 0141905891 scopus 로고    scopus 로고
    • Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    • Haas, B. J., A. L. Delcher, S. M. Mount, J. R. Wortman, R. K. Smith, Jr et al., 2003 Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31: 5654-5666.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5654-5666
    • Haas, B.J.1    Delcher, A.L.2    Mount, S.M.3    Wortman, J.R.4    Smith Jr., R.K.5
  • 20
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang, X., and A. Madan, 1999 CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 21
    • 70949107580 scopus 로고    scopus 로고
    • Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B
    • Iniguez-Luy, F. L., L. Lukens, M. W. Farnham, R. M. Amasino and T. C. Osborn, 2009 Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea. Theor. Appl. Genet. 120: 31-43.
    • (2009) oleracea. Theor. Appl. Genet , vol.120 , pp. 31-43
    • Iniguez-Luy, F.L.1    Lukens, L.2    Farnham, M.W.3    Amasino, R.M.4    Osborn, T.C.5
  • 22
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M., and S. Goto, 2000 KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 23
    • 84879984347 scopus 로고    scopus 로고
    • Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.
    • Koenig, D., J. M. Jimenez-Gomez, S. Kimura, D. Fulop, D. H. Chitwood et al., 2013 Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc. Natl. Acad. Sci. USA 110: E2655-E2662.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. E2655-E2662
    • Koenig, D.1    Jimenez-Gomez, J.M.2    Kimura, S.3    Fulop, D.4    Chitwood, D.H.5
  • 25
    • 84863596169 scopus 로고    scopus 로고
    • Single nucleotide polymorphism discovery from wheat next-generation sequence data
    • Lai, K., C. Duran, P. J. Berkman, M. T. Lorenc, J. Stiller et al., 2012 Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol. J. 10: 743-749.
    • (2012) Plant Biotechnol. J , vol.10 , pp. 743-749
    • Lai, K.1    Duran, C.2    Berkman, P.J.3    Lorenc, M.T.4    Stiller, J.5
  • 26
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform.
    • Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 28
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
    • Majoros, W. H., M. Pertea, and S. L. Salzberg, 2004 TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20: 2878-2879.
    • (2004) Bioinformatics , vol.20 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 29
    • 0029659312 scopus 로고    scopus 로고
    • Pleiotropy causes long-term genetic constraints on life-history evolution in Brassica rapa.
    • Mitchell-Olds, T., 1996 Pleiotropy causes long-term genetic constraints on life-history evolution in Brassica rapa. Evolution 50: 1849-1858.
    • (1996) Evolution , vol.50 , pp. 1849-1858
    • Mitchell-Olds, T.1
  • 30
    • 0002507887 scopus 로고
    • Taxonomy, cytogenetics and origin of crop Brassicas, a review
    • Prakash, S. H., K, 1980 Taxonomy, cytogenetics and origin of crop Brassicas, a review. Opera Bot. 55: 1-57.
    • (1980) Opera Bot , vol.55 , pp. 1-57
    • Prakash, S.H.K.1
  • 31
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K. D., T. Tatusova, and D. R. Maglott, 2007 NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35: D61-D65.
    • (2007) Nucleic Acids Res , vol.35 , pp. D61-D65
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 32
    • 79956319465 scopus 로고    scopus 로고
    • Comparative functional genomics of the fission yeasts.
    • Rhind, N., Z. Chen, M. Yassour, D. A. Thompson, B. J. Haas et al., 2011 Comparative functional genomics of the fission yeasts. Science 332: 930-936.
    • (2011) Science , vol.332 , pp. 930-936
    • Rhind, N.1    Chen, Z.2    Yassour, M.3    Thompson, D.A.4    Haas, B.J.5
  • 33
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov, A. A., and V. V. Solovyev, 2000 Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516-522.
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 34
    • 34548152965 scopus 로고    scopus 로고
    • Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes
    • Schneider, K., D. Kulosa, T. R. Soerensen, S. Mohring, M. Heine et al., 2007 Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor. Appl. Genet. 115: 601-615.
    • (2007) Theor. Appl. Genet , vol.115 , pp. 601-615
    • Schneider, K.1    Kulosa, D.2    Soerensen, T.R.3    Mohring, S.4    Heine, M.5
  • 35
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
    • Schulz, M. H., D. R. Zerbino, M. Vingron, and E. Birney, 2012 Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 36
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J., and H. Ji, 2008 Next-generation DNA sequencing. Nat. Biotechnol. 26: 1135-1145.
    • (2008) Nat. Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 37
    • 78649294100 scopus 로고    scopus 로고
    • Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Surget-Groba, Y., and J. I. Montoya-Burgos, 2010 Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 20: 1432-1440.
    • (2010) Genome Res , vol.20 , pp. 1432-1440
    • Surget-Groba, Y.1    Montoya-Burgos, J.I.2
  • 38
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    • Thorvaldsdottir, H., J. T. Robinson, and J. P. Mesirov, 2013 Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14: 178-192.
    • (2013) Brief. Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 39
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq.
    • Trapnell, C., L. Pachter, and S. L. Salzberg, 2009 TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 40
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C., B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan et al., 2010 Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28: 511-515.
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 41
    • 64749090107 scopus 로고    scopus 로고
    • Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
    • Trick, M., Y. Long, J. Meng, and I. Bancroft, 2009 Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol. J. 7: 334-346.
    • (2009) Plant Biotechnol. J , vol.7 , pp. 334-346
    • Trick, M.1    Long, Y.2    Meng, J.3    Bancroft, I.4
  • 43
    • 80053386792 scopus 로고    scopus 로고
    • The genome of the mesopolyploid crop species Brassica rapa
    • Wang, X., H. Wang, J. Wang, R. Sun, J. Wu et al., 2011 The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43: 1035-1039.
    • (2011) Nat. Genet , vol.43 , pp. 1035-1039
    • Wang, X.1    Wang, H.2    Wang, J.3    Sun, R.4    Wu, J.5
  • 44
  • 45
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R., and E. Birney, 2008 Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.