메뉴 건너뛰기




Volumn 1069, Issue , 2013, Pages 43-58

RNA-Seq for transcriptome analysis in non-model plants

Author keywords

Assembly; Expression analysis; Next generation sequencing; Quality control; RNA seq; Transcriptome

Indexed keywords

RIBOSOME RNA; TRANSCRIPTOME;

EID: 84884179514     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-613-9_4     Document Type: Article
Times cited : (59)

References (45)
  • 1
    • 70350218818 scopus 로고    scopus 로고
    • Applications of new sequencing technologies for transcriptome analysis
    • Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135-151
    • (2009) Annu Rev Genomics Hum Genet , vol.10 , pp. 135-151
    • Morozova, O.1    Hirst, M.2    Marra, M.A.3
  • 2
  • 3
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87-98
    • (2011) Nat Rev Genet , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 4
    • 84857219324 scopus 로고    scopus 로고
    • Next-generation sequencing technologies for gene expression profiling in plants
    • Jain M (2012) Next-generation sequencing technologies for gene expression profiling in plants. Brief Funct Genomics 11:63-70
    • (2012) Brief Funct Genomics , vol.11 , pp. 63-70
    • Jain, M.1
  • 5
    • 70350630320 scopus 로고    scopus 로고
    • Three sequenced legume genomes and many crop species: Rich opportunities for translational genomics
    • Cannon SB, May GD, Jackson SA (2009) Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. Plant Physiol 151:970-977
    • (2009) Plant Physiol , vol.151 , pp. 970-977
    • Cannon, S.B.1    May, G.D.2    Jackson, S.A.3
  • 7
    • 79961197602 scopus 로고    scopus 로고
    • Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development
    • Garg R, Patel RK, Jhanwar S et al (2011) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol 156:1661-1678
    • (2011) Plant Physiol , vol.156 , pp. 1661-1678
    • Garg, R.1    Patel, R.K.2    Jhanwar, S.3
  • 8
    • 84871481001 scopus 로고    scopus 로고
    • Genome-enabled insights into legume biology
    • Young ND, Bharti AK (2012) Genome-enabled insights into legume biology. Annu Rev Plant Biol 63:283-305
    • (2012) Annu Rev Plant Biol , vol.63 , pp. 283-305
    • Young, N.D.1    Bharti, A.K.2
  • 9
    • 0037353554 scopus 로고    scopus 로고
    • Legumes: Importance and constraints to greater use
    • Graham PH, Vance CP (2003) Legumes: importance and constraints to greater use. Plant Physiol 131:872-877
    • (2003) Plant Physiol , vol.131 , pp. 872-877
    • Graham, P.H.1    Vance, C.P.2
  • 10
    • 84860776638 scopus 로고    scopus 로고
    • A next generation approach to the characterization of a non-model plant transcriptome
    • Jain M (2011) A next generation approach to the characterization of a non-model plant transcriptome. Curr Sci 101:1435-1439
    • (2011) Curr Sci , vol.101 , pp. 1435-1439
    • Jain, M.1
  • 11
    • 84858608318 scopus 로고    scopus 로고
    • Designing a transcriptome next-generation sequencing project for a nonmodel plant species
    • Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am J Bot 99:257-266
    • (2012) Am J Bot , vol.99 , pp. 257-266
    • Strickler, S.R.1    Bombarely, A.2    Mueller, L.A.3
  • 12
    • 79951828683 scopus 로고    scopus 로고
    • De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification
    • Garg R, Patel RK, Tyagi AK et al (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53-63
    • (2011) DNA Res , vol.18 , pp. 53-63
    • Garg, R.1    Patel, R.K.2    Tyagi, A.K.3
  • 14
    • 39649117755 scopus 로고    scopus 로고
    • The impact of nextgeneration sequencing technology on genetics
    • Mardis ER (2008) The impact of nextgeneration sequencing technology on genetics. Trends Genet 24:133-141
    • (2008) Trends Genet , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 15
    • 53649088131 scopus 로고    scopus 로고
    • Applications of next-generation sequencing technologies in functional genomics
    • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264
    • (2008) Genomics , vol.92 , pp. 255-264
    • Morozova, O.1    Marra, M.A.2
  • 16
    • 67651033745 scopus 로고    scopus 로고
    • Short-read sequencing technologies for transcriptional analyses
    • Simon SA, Zhai J, Nandety RS et al (2009) Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Biol 60: 305-333
    • (2009) Annu Rev Plant Biol , vol.60 , pp. 305-333
    • Simon, S.A.1    Zhai, J.2    Nandety, R.S.3
  • 18
    • 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
  • 20
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: At-A-glance quality assessment of illumina second-generation sequencing data
    • Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of illumina second-generation sequencing data. BMC Bioinformatics 11:485
    • (2010) BMC Bioinformatics , vol.11 , pp. 485
    • Cox, M.P.1    Peterson, D.A.2    Biggs, P.J.3
  • 21
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863-864
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 22
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315-327
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 23
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682
    • (2011) Nat Rev Genet , vol.12 , pp. 671-682
    • Martin, J.A.1    Wang, Z.2
  • 24
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman M, Garbe RM, Levin JZ et al (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28:503-510
    • (2010) Nat Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1    Garbe, R.M.2    Levin, J.Z.3
  • 25
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G 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
  • 26
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562-578
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3
  • 27
    • 79960892661 scopus 로고    scopus 로고
    • De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity
    • Iorizzo M, Senalik DA, Grzebelus D et al (2011) De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12:389
    • (2011) BMC Genomics , vol.12 , pp. 389
    • Iorizzo, M.1    Senalik, D.A.2    Grzebelus, D.3
  • 28
    • 80052611733 scopus 로고    scopus 로고
    • RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis
    • Xia Z, Xu H, Zhai J et al (2011) RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 77: 299-308
    • (2011) Plant Mol Biol , vol.77 , pp. 299-308
    • Xia, Z.1    Xu, H.2    Zhai, J.3
  • 29
    • 84860485003 scopus 로고    scopus 로고
    • Optimizing de novo transcriptome assembly from short-read RNA-Seq data: A comparative study
    • Zhao QY, Wang Y, Kong YM et al (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12(Suppl 14):S2
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 14
    • Zhao, Q.Y.1    Wang, Y.2    Kong, Y.M.3
  • 30
    • 84860491097 scopus 로고    scopus 로고
    • Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]
    • Tao X, Gu YH, Wang HY et al (2012) Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [ Ipomoea batatas (L.) Lam]. PLoS One 7: e36234
    • (2012) PLoS One , vol.7
    • Tao, X.1    Gu, Y.H.2    Wang, H.Y.3
  • 31
    • 84859061827 scopus 로고    scopus 로고
    • Exploring the switchgrass transcriptome using secondgeneration sequencing technology
    • Wang Y, Zeng X, Iyer NJ et al (2012) Exploring the switchgrass transcriptome using secondgeneration sequencing technology. PLoS One 7:e34225
    • (2012) PLoS One , vol.7
    • Wang, Y.1    Zeng, X.2    Iyer, N.J.3
  • 32
    • 84863567245 scopus 로고    scopus 로고
    • Transcriptome sequencing of wild chickpea as a rich resource for marker development
    • Jhanwar S, Priya P, Garg R et al (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol J 10:690-702
    • (2012) Plant Biotechnol J , vol.10 , pp. 690-702
    • Jhanwar, S.1    Priya, P.2    Garg, R.3
  • 33
    • 0034882994 scopus 로고    scopus 로고
    • Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential
    • Temnykh S, DeClerck G, Lukashova A et al (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441-1452
    • (2001) Genome Res , vol.11 , pp. 1441-1452
    • Temnykh, S.1    Declerck, G.2    Lukashova, A.3
  • 34
    • 0037854629 scopus 로고    scopus 로고
    • Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    • Thiel T, Michalek W, Varshney RK et al (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422
    • (2003) Theor Appl Genet , vol.106 , pp. 411-422
    • Thiel, T.1    Michalek, W.2    Varshney, R.K.3
  • 35
    • 34250666153 scopus 로고    scopus 로고
    • Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing
    • Weber AP, Weber KL, Carr K et al (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144:32-42
    • (2007) Plant Physiol , vol.144 , pp. 32-42
    • Weber, A.P.1    Weber, K.L.2    Carr, K.3
  • 36
    • 57749195712 scopus 로고    scopus 로고
    • RNASeq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M (2009) RNASeq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 37
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E (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
  • 38
    • 84859768479 scopus 로고    scopus 로고
    • Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz MH, Zerbino DR, Vingron M et al (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
  • 39
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson JT, Wong K, Jackman SD et al (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117-1123
    • (2009) Genome Res , vol.19 , pp. 1117-1123
    • Simpson, J.T.1    Wong, K.2    Jackman, S.D.3
  • 40
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    • Chevreux B, Pfisterer T, Drescher B et al (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147-1159
    • (2004) Genome Res , vol.14 , pp. 1147-1159
    • Chevreux, B.1    Pfisterer, T.2    Drescher, B.3
  • 41
    • 0037460985 scopus 로고    scopus 로고
    • TIGR Gene Indices clustering tools (TGICL): A software system for fast clustering of large EST datasets
    • Pertea G, Huang X, Liang F et al (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651-652
    • (2003) Bioinformatics , vol.19 , pp. 651-652
    • Pertea, G.1    Huang, X.2    Liang, F.3
  • 42
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A (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
  • 43
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 44
    • 78649294100 scopus 로고    scopus 로고
    • Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Surget-Groba Y, Montoya-Burgos JI (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
  • 45
    • 77957926979 scopus 로고    scopus 로고
    • Comparing de novo assemblers for 454 transcriptome data
    • Kumar S, Blaxter ML (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11:571
    • (2010) BMC Genomics , vol.11 , pp. 571
    • Kumar, S.1    Blaxter, M.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.