title: Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays.
abstract: Transcriptome analysis is a valuable tool for identification and characterization of genes and pathways underlying plant growth and development. We previously published a microarray-based maize gene atlas from the analysis of 60 unique spatially and temporally separated tissues from 11 maize organs [1]. To enhance the coverage and resolution of the maize gene atlas, we have analyzed 18 selected tissues representing five organs using RNA sequencing (RNA-Seq). For a direct comparison of the two methodologies, the same RNA samples originally used for our microarray-based atlas were evaluated using RNA-Seq. Both technologies produced similar transcriptome profiles as evident from high Pearson's correlation statistics ranging from 0.70 to 0.83, and from nearly identical clustering of the tissues. RNA-Seq provided enhanced coverage of the transcriptome, with 82.1% of the filtered maize genes detected as expressed in at least one tissue by RNA-Seq compared to only 56.5% detected by microarrays. Further, from the set of 465 maize genes that have been historically well characterized by mutant analysis, 427 show significant expression in at least one tissue by RNA-Seq compared to 390 by microarray analysis. RNA-Seq provided higher resolution for identifying tissue-specific expression as well as for distinguishing the expression profiles of closely related paralogs as compared to microarray-derived profiles. Co-expression analysis derived from the microarray and RNA-Seq data revealed that broadly similar networks result from both platforms, and that co-expression estimates are stable even when constructed from mixed data including both RNA-Seq and microarray expression data. The RNA-Seq information provides a useful complement to the microarray-based maize gene atlas and helps to further understand the dynamics of transcription during maize development.
authors: Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America.
authors: Rajandeep S
authors: RS
authors: Sekhon
authors: Roman
authors: R
authors: Briskine
authors: Candice N
authors: CN
authors: Hirsch
authors: Chad L
authors: CL
authors: Myers
authors: Nathan M
authors: NM
authors: Springer
authors: C Robin
authors: CR
authors: Buell
authors: Natalia
authors: N
authors: de Leon
authors: Shawn M
authors: SM
authors: Kaeppler
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA; D003313:Zea mays / Q000235:genetics*
references: BMC Plant Biol. 2010 Aug 05;10:160
references: 20687943
references: Nat Genet. 2005 May;37(5):501-6
references: 15806101
references: Database (Oxford). 2011 May 29;2011:bar022
references: 21624896
references: Development. 1990 Nov;110(3):985-1000
references: 2088734
references: Plant Cell. 2004;16 Suppl:S203-13
references: 15010515
references: Genome Res. 2008 Sep;18(9):1509-17
references: 18550803
references: Plant Biotechnol J. 2006 Sep;4(5):489-98
references: 17309725
references: Plant Physiol. 2003 Aug;132(4):1739-54
references: 12913132
references: Plant Physiol. 2003 Feb;131(2):568-82
references: 12586881
references: Bioinformatics. 2006 Dec 1;22(23):2890-7
references: 17005538
references: Funct Integr Genomics. 2002 May;2(1-2):13-27
references: 12021847
references: PLoS Biol. 2007 May;5(5):e129
references: 17439305
references: Funct Integr Genomics. 2006 Jul;6(3):202-11
references: 16547597
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Plant Physiol. 2001 Sep;127(1):173-83
references: 11553745
references: Nat Biotechnol. 2010 May;28(5):511-5
references: 20436464
references: Plant J. 2011 May;66(4):553-63
references: 21299659
references: Bioinformatics. 2008 Jul 1;24(13):1559-61
references: 18499696
references: Science. 2009 Nov 20;326(5956):1112-5
references: 19965430
references: J Mol Evol. 2007 Sep;65(3):316-27
references: 17846820
references: Genes Dev. 1996 Dec 1;10(23):3018-27
references: 8957002
references: Plant Cell. 1993 Dec;5(12):1795-805
references: 8305872
references: PLoS Pathog. 2009 Feb;5(2):e1000290
references: 19197359
references: PLoS One. 2012;7(3):e33071
references: 22438891
references: Plant Mol Biol. 2010 Mar;72(4-5):407-21
references: 19953304
references: Mol Gen Genet. 1994 May 25;243(4):400-8
references: 8202085
references: BMC Genomics. 2006 Jan 19;7:10
references: 16423292
references: Plant Physiol. 1994 Jan;104(1):179-87
references: 8115545
references: Genome Res. 2010 May;20(5):646-54
references: 20305017
references: Nat Genet. 2009 Feb;41(2):258-63
references: 19122662
references: Plant J. 2008 Aug;55(3):504-13
references: 18410479
references: Genome Biol. 2004;5(3):R16
references: 15003119
references: Genome Res. 2000 Apr;10(4):516-22
references: 10779491
references: Genetics. 2003 Mar;163(3):1109-22
references: 12663548
references: Genome Res. 2010 Sep;20(9):1238-49
references: 20627892
references: Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4069-74
references: 21368132
references: Nat Rev Genet. 2009 Jan;10(1):57-63
references: 19015660
references: Bioinformatics. 2009 May 1;25(9):1105-11
references: 19289445
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: Plant Cell. 1995 Apr;7(4):407-16
references: 7773015
references: Genome Biol Evol. 2012;4(3):265-77
references: 22275519
references: Plant Physiol. 2009 Jan;149(1):14-26
references: 19126691
references: Genome Biol. 2005;6(4):R33
references: 15833120
references: Genome Res. 2010 Jan;20(1):45-58
references: 19858364
references: Nat Genet. 2010 Dec;42(12):1060-7
references: 21037569
references: PLoS One. 2011 Mar 10;6(3):e17855
references: 21423772
references: Plant Physiol. 2010 Nov;154(3):1024-39
references: 20833728
references: Plant J. 2010 Jul 1;63(1):86-99
references: 20408999
references: Plant Mol Biol. 2005 May;58(2):269-82
references: 16027978