title: Catalyzing plant science research with RNA-seq.
abstract: Next generation DNA sequencing technologies are driving increasingly rapid, affordable and high resolution analyses of plant transcriptomes through sequencing of their associated cDNA (complementary DNA) populations; an analytical platform commonly referred to as RNA-sequencing (RNA-seq). Since entering the arena of whole genome profiling technologies only a few years ago, RNA-seq has proven itself to be a powerful tool with a remarkably diverse range of applications, from detailed studies of biological processes at the cell type-specific level, to providing insights into fundamental questions in plant biology on an evolutionary time scale. Applications include generating genomic data for heretofore unsequenced species, thus expanding the boundaries of what had been considered "model organisms," elucidating structural and regulatory gene networks, revealing how plants respond to developmental cues and their environment, allowing a better understanding of the relationships between genes and their products, and uniting the "omics" fields of transcriptomics, proteomics, and metabolomics into a now common systems biology paradigm. We provide an overview of the breadth of such studies and summarize the range of RNA-seq protocols that have been developed to address questions spanning cell type-specific-based transcriptomics, transcript secondary structure and gene mapping.
authors.affiliation: Department of Plant Biology, Cornell University Ithaca, NY, USA.
authors.forename: Laetitia B B
authors.initials: LB
authors.lastname: Martin
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: James J
authors.initials: JJ
authors.lastname: Giovannoni
authors.forename: Jocelyn K C
authors.initials: JK
authors.lastname: Rose
keywords: RNA-seq; next generation sequencing; plant transcriptome; systems biology; transcriptomics
references.citation: Plant J. 2012 Apr;70(1):5-17
references.pmid: 22449039
references.citation: BMC Genomics. 2011 Dec 13;12:600
references.pmid: 22151917
references.citation: BMC Genomics. 2011 Feb 08;12:99
references.pmid: 21303537
references.citation: Nat Biotechnol. 2012 Aug;30(8):798-802
references.pmid: 22820317
references.citation: BMC Genomics. 2010 Jul 13;11:431
references.pmid: 20626894
references.citation: BMC Genomics. 2008 Dec 09;9:593
references.pmid: 19068109
references.citation: Nat Methods. 2010 Sep;7(9):709-15
references.pmid: 20711195
references.citation: PLoS Genet. 2011 Jun;7(6):e1002125
references.pmid: 21731498
references.citation: Nature. 2000 Dec 14;408(6814):796-815
references.pmid: 11130711
references.citation: Genome Res. 2012 Jun;22(6):1184-95
references.pmid: 22391557
references.citation: Nature. 2010 Mar 11;464(7286):250-5
references.pmid: 20164839
references.citation: RNA Biol. 2011 May-Jun;8(3):404-14
references.pmid: 21525783
references.citation: Science. 2005 Sep 2;309(5740):1567-9
references.pmid: 16141074
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12527-32
references.pmid: 21709233
references.citation: BMC Genomics. 2009 Aug 26;10:399
references.pmid: 19709400
references.citation: DNA Res. 2011 Dec;18(6):483-97
references.pmid: 21987089
references.citation: Plant Physiol. 2012 Oct;160(2):846-67
references.pmid: 22837360
references.citation: Plant J. 2012 Aug;71(3):492-502
references.pmid: 22443345
references.citation: Nature. 2004 Sep 16;431(7006):356-63
references.pmid: 15372043
references.citation: Plant Cell. 2003 Mar;15(3):583-96
references.pmid: 12615934
references.citation: Plant Physiol. 2008 Mar;146(3):1305-21
references.pmid: 18192438
references.citation: Science. 2010 Jan 1;327(5961):94-7
references.pmid: 19965720
references.citation: BMC Plant Biol. 2010 Dec 17;10:280
references.pmid: 21167045
references.citation: RNA. 2011 Mar;17(3):390-400
references.pmid: 21220549
references.citation: Plant Mol Biol. 2011 May;76(1-2):1-18
references.pmid: 21387125
references.citation: Bioinformatics. 2012 Jun 15;28(12):1592-7
references.pmid: 22556371
references.citation: BMC Bioinformatics. 2009 Oct 21;10:346
references.pmid: 19845953
references.citation: PLoS Genet. 2010 Sep 30;6(9):e1001141
references.pmid: 20941385
references.citation: Nucleic Acids Res. 2003 May 15;31(10):2601-13
references.pmid: 12736310
references.citation: Plant Physiol. 2010 Apr;152(4):1787-95
references.pmid: 20118272
references.citation: Science. 2003 Dec 12;302(5652):1956-60
references.pmid: 14671301
references.citation: PLoS Genet. 2009 May;5(5):e1000476
references.pmid: 19424435
references.citation: BMC Plant Biol. 2009 May 09;9:51
references.pmid: 19426529
references.citation: Cell. 2008 May 2;133(3):523-36
references.pmid: 18423832
references.citation: Plant J. 2004 Sep;39(5):697-714
references.pmid: 15315633
references.citation: Plant J. 2012 May;70(3):421-31
references.pmid: 22247970
references.citation: PLoS One. 2011;6(10):e26426
references.pmid: 22039485
references.citation: Genome Res. 2008 Dec;18(12):2024-33
references.pmid: 18818371
references.citation: Plant J. 2010 Jun 1;62(6):960-76
references.pmid: 20230504
references.citation: PLoS One. 2011;6(6):e21220
references.pmid: 21731678
references.citation: BMC Genomics. 2012 Jul 16;13:316
references.pmid: 22800194
references.citation: BMC Genomics. 2010 Dec 01;11:681
references.pmid: 21122097
references.citation: Front Plant Sci. 2012 Sep 25;3:220
references.pmid: 23056003
references.citation: BMC Plant Biol. 2009 Oct 23;9:127
references.pmid: 19852773
references.citation: Plant Cell. 2012 Jan;24(1):123-36
references.pmid: 22267485
references.citation: Cold Spring Harb Protoc. 2011 Aug 01;2011(8):940-9
references.pmid: 21807852
references.citation: Genome Res. 2010 Sep;20(9):1238-49
references.pmid: 20627892
references.citation: Plant Cell Rep. 2012 Aug;31(8):1437-47
references.pmid: 22476438
references.citation: Plant Physiol. 2003 Jun;132(2):469-84
references.pmid: 12805580
references.citation: BMC Plant Biol. 2011 Sep 28;11:131
references.pmid: 21951788
references.citation: Plant Cell. 2011 Nov;23(11):3893-910
references.pmid: 22045915
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9
references.pmid: 16845059
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1755-62
references.pmid: 21257907
references.citation: Nature. 2011 Aug 28;477(7365):419-23
references.pmid: 21874022
references.citation: Plant Cell. 2012 Aug;24(8):3219-34
references.pmid: 22911570
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: BMC Genomics. 2009 Sep 23;10:449
references.pmid: 19772667
references.citation: Trends Plant Sci. 2012 Jan;17(1):16-21
references.pmid: 22104407
references.citation: BMC Plant Biol. 2012 Jul 29;12:121
references.pmid: 22838966
references.citation: Science. 2005 Sep 2;309(5740):1519-24
references.pmid: 16141061
references.citation: Plant Physiol. 2007 May;144(1):32-42
references.pmid: 17351049
references.citation: Nature. 2008 Mar 13;452(7184):215-9
references.pmid: 18278030
references.citation: Plant Physiol. 2009 Dec;151(4):2120-32
references.pmid: 19854858
references.citation: Proteomics. 2012 Mar;12(6):761-74
references.pmid: 22539427
references.citation: PLoS One. 2011;6(8):e23687
references.pmid: 21858209
references.citation: BMC Genomics. 2011 Jul 08;12:356
references.pmid: 21740560
references.citation: Plant Physiol. 2009 Mar;149(3):1316-24
references.pmid: 19118127
references.citation: Nat Rev Genet. 2011 Feb;12(2):87-98
references.pmid: 21191423
references.citation: J Comput Biol. 2012 Jun;19(6):710-30
references.pmid: 22697243
references.citation: Plant Mol Biol. 2012 Jun;79(3):295-313
references.pmid: 22527754
references.citation: New Phytol. 2009 Aug;183(3):764-775
references.pmid: 19549131
references.citation: BMC Genomics. 2011 Oct 18;12:514
references.pmid: 22008187
references.citation: Nat Biotechnol. 2013 Feb;31(2):154-9
references.pmid: 23354102
references.citation: PLoS One. 2011;6(7):e22196
references.pmid: 21799793
references.citation: Plant Cell Rep. 2012 Oct;31(10):1823-8
references.pmid: 22684307
references.citation: PLoS Comput Biol. 2009 Dec;5(12):e1000598
references.pmid: 20011106
references.citation: PLoS One. 2012;7(10):e46703
references.pmid: 23071617
references.citation: Cell. 2009 Feb 20;136(4):629-41
references.pmid: 19239885
references.citation: PLoS One. 2011;6(12):e29335
references.pmid: 22216251
references.citation: Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20042-7
references.pmid: 22114195
references.citation: Front Plant Sci. 2012 Nov 08;3:248
references.pmid: 23162560
references.citation: Plant Physiol. 2011 May;156(1):330-45
references.pmid: 21398260
references.citation: Plant Physiol. 2006 Apr;140(4):1192-204
references.pmid: 16500993
references.citation: Genome Res. 2010 Jan;20(1):45-58
references.pmid: 19858364
references.citation: Am J Bot. 2012 Feb;99(2):383-96
references.pmid: 22301896
references.citation: Plant Physiol. 2011 Aug;156(4):1661-78
references.pmid: 21653784
references.citation: PLoS One. 2012;7(5):e36406
references.pmid: 22586469
references.citation: PLoS One. 2012;7(6):e38653
references.pmid: 22723874
references.citation: Plant Physiol. 2011 Jan;155(1):142-56
references.pmid: 20543093
references.citation: Genes (Basel). 2012 Mar 08;3(1):176-90
references.pmid: 24704849
references.citation: Genome Biol. 2012 Jun 15;13(6):R47
references.pmid: 22704043
references.citation: BMC Genomics. 2011 May 11;12:227
references.pmid: 21569327
references.citation: Genome Res. 2008 Oct;18(10):1602-9
references.pmid: 18653800
references.citation: DNA Res. 2012;19(1):1-9
references.pmid: 22039173
references.citation: Nucleic Acids Res. 2009 Oct;37(18):e123
references.pmid: 19620212
references.citation: Plant Cell. 2010 Jun;22(6):2058-84
references.pmid: 20587772
references.citation: Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18729-34
references.pmid: 20937895
references.citation: Genome Res. 2012 Jan;22(1):163-76
references.pmid: 21940835
references.citation: J Exp Bot. 2010 Jul;61(12):3321-30
references.pmid: 20519339