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Volumn 169, Issue 3, 2015, Pages 1524-1531

Discovering new biology through sequencing of RNA

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA;

EID: 84946227814     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.15.01081     Document Type: Article
Times cited : (34)

References (70)
  • 1
    • 84903442051 scopus 로고    scopus 로고
    • Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis
    • Aubry S, Kelly S, Kümpers BMC, Smith-Unna RD, Hibberd JM (2014a) Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS Genet 10: e1004365
    • (2014) Plos Genet , pp. 10
    • Aubry, S.1    Kelly, S.2    Kümpers, B.3    Smith-Unna, R.D.4    Hibberd, J.M.5
  • 2
    • 84900468244 scopus 로고    scopus 로고
    • Transcript residency on ribosomes reveals a key role for the Arabidopsis thaliana bundle sheath in sulfur and glucosinolate metabolism
    • Aubry S, Smith-Unna RD, Boursnell CM, Kopriva S, Hibberd JM (2014b) Transcript residency on ribosomes reveals a key role for the Arabidopsis thaliana bundle sheath in sulfur and glucosinolate metabolism. Plant J 78: 659–673
    • (2014) Plant J , vol.78 , pp. 659-673
    • Aubry, S.1    Smith-Unna, R.D.2    Boursnell, C.M.3    Kopriva, S.4    Hibberd, J.M.5
  • 7
    • 55549093447 scopus 로고    scopus 로고
    • Comparative proteomics of chloroplast envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes
    • Bräutigam A, Hoffmann-Benning S, Weber AP (2008a) Comparative proteomics of chloroplast envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes. Plant Physiol 148: 568–579
    • (2008) Plant Physiol , vol.148 , pp. 568-579
    • Bräutigam, A.1    Hoffmann-Benning, S.2    Weber, A.P.3
  • 9
    • 79957543095 scopus 로고    scopus 로고
    • Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species
    • Bräutigam A, Mullick T, Schliesky S, Weber APM (2011b) Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species. J Exp Bot 62: 3093–3102
    • (2011) J Exp Bot , vol.62 , pp. 3093-3102
    • Bräutigam, A.1    Mullick, T.2    Schliesky, S.3    Weber, A.4
  • 10
    • 84907460946 scopus 로고    scopus 로고
    • Towards an integrative model of C4 photosynthetic subtypes: Insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species
    • Bräutigam A, Schliesky S, Külahoglu C, Osborne CP, Weber APM (2014) Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. J Exp Bot 65: 3579–3593
    • (2014) J Exp Bot , vol.65 , pp. 3579-3593
    • Bräutigam, A.1    Schliesky, S.2    Külahoglu, C.3    Osborne, C.P.4    Weber, A.5
  • 11
    • 49949089949 scopus 로고    scopus 로고
    • Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: Comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes
    • Bräutigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE, Weber APM (2008b) Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. J Biotechnol 136: 44–53
    • (2008) J Biotechnol , vol.136 , pp. 44-53
    • Bräutigam, A.1    Shrestha, R.P.2    Whitten, D.3    Wilkerson, C.G.4    Carr, K.M.5    Froehlich, J.E.6    Weber, A.7
  • 12
    • 33751017957 scopus 로고    scopus 로고
    • Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    • Cheung F, Haas BJ, Goldberg SMD, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7: 272
    • (2006) BMC Genomics , vol.7 , pp. 272
    • Cheung, F.1    Haas, B.J.2    Goldberg, S.3    May, G.D.4    Xiao, Y.5    Town, C.D.6
  • 14
    • 84893116505 scopus 로고    scopus 로고
    • The high polyphenol content of grapevine cultivar Tannat berries is conferred primarily by genes that are not shared with the reference genome
    • Da Silva C, Zamperin G, Ferrarini A, Minio A, Dal Molin A, Venturini L, Buson G, Tononi P, Avanzato C, Zago E, et al (2013) The high polyphenol content of grapevine cultivar Tannat berries is conferred primarily by genes that are not shared with the reference genome. Plant Cell 25: 4777–4788
    • (2013) Plant Cell , vol.25 , pp. 4777-4788
    • Da Silva, C.1    Zamperin, G.2    Ferrarini, A.3    Minio, A.4    Dal Molin, A.5    Venturini, L.6    Buson, G.7    Tononi, P.8    Avanzato, C.9    Zago, E.10
  • 15
    • 33845984917 scopus 로고    scopus 로고
    • Gene discovery and annotation using LCM-454 transcriptome sequencing
    • Emrich SJ, Barbazuk WB, Li L, Schnable PS (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17: 69–73
    • (2007) Genome Res , vol.17 , pp. 69-73
    • Emrich, S.J.1    Barbazuk, W.B.2    Li, L.3    Schnable, P.S.4
  • 16
    • 84903178904 scopus 로고    scopus 로고
    • Cracking the Kranz enigma with systems biology
    • Fouracre JP, Ando S, Langdale JA (2014) Cracking the Kranz enigma with systems biology. J Exp Bot 65: 3327–3339
    • (2014) J Exp Bot , vol.65 , pp. 3327-3339
    • Fouracre, J.P.1    Ando, S.2    Langdale, J.A.3
  • 18
    • 84946197772 scopus 로고    scopus 로고
    • Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
    • Gaidatzis D, Burger L, Florescu M, Stadler MB (2015) Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol 33: 722–729
    • (2015) Nat Biotechnol , vol.33 , pp. 722-729
    • Gaidatzis, D.1    Burger, L.2    Florescu, M.3    Stadler, M.B.4
  • 20
    • 79960866455 scopus 로고    scopus 로고
    • Evolution of C4 photosynthesis in the genus Flaveria: How many and which genes does it take to make C4?
    • Gowik U, Bräutigam A, Weber KL, Weber APM, Westhoff P (2011) Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? Plant Cell 23: 2087–2105
    • (2011) Plant Cell , vol.23 , pp. 2087-2105
    • Gowik, U.1    Bräutigam, A.2    Weber, K.L.3    Weber, A.4    Westhoff, P.5
  • 27
    • 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
  • 28
    • 84864709312 scopus 로고    scopus 로고
    • RNASeq analysis of developing nasturtium seeds (Tropaeolum majus): Identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis
    • Jensen JK, Schultink A, Keegstra K, Wilkerson CG, Pauly M (2012) RNASeq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis. Mol Plant 5: 984–992
    • (2012) Mol Plant , vol.5 , pp. 984-992
    • Jensen, J.K.1    Schultink, A.2    Keegstra, K.3    Wilkerson, C.G.4    Pauly, M.5
  • 29
    • 84899830018 scopus 로고    scopus 로고
    • Evolutionary convergence of cell-specific gene expression in independent lineages of C4 grasses
    • John CR, Smith-Unna RD, Woodfield H, Covshoff S, Hibberd JM (2014) Evolutionary convergence of cell-specific gene expression in independent lineages of C4 grasses. Plant Physiol 165: 62–75
    • (2014) Plant Physiol , vol.165 , pp. 62-75
    • John, C.R.1    Smith-Unna, R.D.2    Woodfield, H.3    Covshoff, S.4    Hibberd, J.M.5
  • 30
    • 0036226603 scopus 로고    scopus 로고
    • BLAT–the BLAST-like alignment tool
    • Kent WJ (2002) BLAT–the BLAST-like alignment tool. Genome Res 12: 656–664
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 32
    • 84922432978 scopus 로고    scopus 로고
    • The devil in the details of RNA-seq
    • Kratz A, Carninci P (2014) The devil in the details of RNA-seq. Nat Biotechnol 32: 882–884
    • (2014) Nat Biotechnol , vol.32 , pp. 882-884
    • Kratz, A.1    Carninci, P.2
  • 33
    • 84897410582 scopus 로고    scopus 로고
    • Points of significance: Comparing samples - Part II
    • Krzywinski M, Altman N (2014) Points of significance: comparing samples - part II. Nat Methods 11: 355–356
    • (2014) Nat Methods , vol.11 , pp. 355-356
    • Krzywinski, M.1    Altman, N.2
  • 34
    • 84922395220 scopus 로고    scopus 로고
    • Quantitative transcriptome analysis using RNA-seq
    • Külahoglu C, Bräutigam A (2014) Quantitative transcriptome analysis using RNA-seq. Methods Mol Biol 1158: 71–91
    • (2014) Methods Mol Biol , vol.1158 , pp. 71-91
    • Külahoglu, C.1    Bräutigam, A.2
  • 36
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 559
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 37
    • 84859326067 scopus 로고    scopus 로고
    • Fast R functions for robust correlations and hierarchical clustering
    • Langfelder P, Horvath S (2012) Fast R functions for robust correlations and hierarchical clustering. J Stat Softw 46: 46
    • (2012) J Stat Softw , vol.46 , pp. 46
    • Langfelder, P.1    Horvath, S.2
  • 42
    • 84941599050 scopus 로고    scopus 로고
    • The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria
    • Mallmann J, Heckmann D, Bräutigam A, Lercher MJ, Weber AP, Westhoff P, Gowik U (2014) The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria. eLife 3: e02478–e02478
    • (2014) Elife , vol.3 , pp. e02478-e02478
    • Mallmann, J.1    Heckmann, D.2    Bräutigam, A.3    Lercher, M.J.4    Weber, A.P.5    Westhoff, P.6    Gowik, U.7
  • 43
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9: 387–402
    • (2008) Annu Rev Genomics Hum Genet , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 51
    • 84899649317 scopus 로고    scopus 로고
    • Correlation of mRNA and protein abundance in the developing maize leaf
    • Ponnala L, Wang Y, Sun Q, van Wijk KJ (2014) Correlation of mRNA and protein abundance in the developing maize leaf. Plant J 78: 424–440
    • (2014) Plant J , vol.78 , pp. 424-440
    • Ponnala, L.1    Wang, Y.2    Sun, Q.3    Van Wijk, K.J.4
  • 52
    • 84924912185 scopus 로고    scopus 로고
    • Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes
    • Reynoso MA, Juntawong P, Lancia M, Blanco FA, Bailey-Serres J, Zanetti ME (2015) Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes. Methods Mol Biol 1284: 185–207
    • (2015) Methods Mol Biol , vol.1284 , pp. 185-207
    • Reynoso, M.A.1    Juntawong, P.2    Lancia, M.3    Blanco, F.A.4    Bailey-Serres, J.5    Zanetti, M.E.6
  • 53
    • 0032540905 scopus 로고    scopus 로고
    • A sequencing method based on realtime pyrophosphate
    • Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on realtime pyrophosphate. Science 281: 363–365, 365
    • (1998) Science , vol.363-365 , Issue.365 , pp. 281
    • Ronaghi, M.1    Uhlén, M.2    Nyrén, P.3
  • 57
    • 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, Birney E (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
  • 59
    • 84920550975 scopus 로고    scopus 로고
    • A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
    • SEQC/MAQC-III Consortium
    • SEQC/MAQC-III Consortium (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 32: 903–914
    • (2014) Nat Biotechnol , vol.32 , pp. 903-914
  • 60
    • 84887412533 scopus 로고    scopus 로고
    • A single-molecule longread survey of the human transcriptome
    • Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule longread survey of the human transcriptome. Nat Biotechnol 31: 1009–1014
    • (2013) Nat Biotechnol , vol.31 , pp. 1009-1014
    • Sharon, D.1    Tilgner, H.2    Grubert, F.3    Snyder, M.4
  • 62
    • 84904016056 scopus 로고    scopus 로고
    • Defining a personal, allele-specific, and single-molecule long-read transcriptome
    • Tilgner H, Grubert F, Sharon D, Snyder MP (2014) Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci USA 111: 9869–9874
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 9869-9874
    • Tilgner, H.1    Grubert, F.2    Sharon, D.3    Snyder, M.P.4
  • 64
    • 68249092895 scopus 로고    scopus 로고
    • A guide to using MapMan to visualize and compare omics data in plants: A case study in the crop species, maize
    • Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare omics data in plants: a case study in the crop species, maize. Plant Cell Environ 32: 1211–1229
    • (2009) Plant Cell Environ , vol.32 , pp. 1211-1229
    • Usadel, B.1    Poree, F.2    Nagel, A.3    Lohse, M.4    Czedik-Eysenberg, A.5    Stitt, M.6
  • 66
    • 84882454973 scopus 로고    scopus 로고
    • Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy
    • Wang P, Kelly S, Fouracre JP, Langdale JA (2013) Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy. Plant J 75: 656–670
    • (2013) Plant J , vol.75 , pp. 656-670
    • Wang, P.1    Kelly, S.2    Fouracre, J.P.3    Langdale, J.A.4
  • 67
    • 34250666153 scopus 로고    scopus 로고
    • Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing
    • Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32–42
    • (2007) Plant Physiol , vol.144 , pp. 32-42
    • Weber, A.1    Weber, K.L.2    Carr, K.3    Wilkerson, C.4    Ohlrogge, J.B.5
  • 68
    • 33750354315 scopus 로고    scopus 로고
    • Back to the future: Education for systemslevel biologists
    • Wingreen N, Botstein D (2006) Back to the future: education for systemslevel biologists. Nat Rev Mol Cell Biol 7: 829–832
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 829-832
    • Wingreen, N.1    Botstein, D.2
  • 69
    • 84896726932 scopus 로고    scopus 로고
    • Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome
    • Yoo MJ, Wendel JF (2014) Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet 10: e1004073
    • (2014) Plos Genet , pp. 10
    • Yoo, M.J.1    Wendel, J.F.2
  • 70
    • 26944438704 scopus 로고    scopus 로고
    • Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression
    • Zanetti ME, Chang IF, Gong F, Galbraith DW, Bailey-Serres J (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol 138: 624–635
    • (2005) Plant Physiol , vol.138 , pp. 624-635
    • Zanetti, M.E.1    Chang, I.F.2    Gong, F.3    Galbraith, D.W.4    Bailey-Serres, J.5


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