title: De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission.
abstract: Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel; The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel.
authors.forename: Srivignesh
authors.initials: S
authors.lastname: Sundaresan
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center Bet-Dagan, Israel.
authors.forename: Sonia
authors.initials: S
authors.lastname: Philosoph-Hadas
authors.affiliation: The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem Rehovot, Israel.
authors.forename: Joseph
authors.initials: J
authors.lastname: Riov
authors.affiliation: Department of Bioinformatics, QTLomics Technologies Pvt. Ltd Bangalore, India.
authors.forename: Raja
authors.initials: R
authors.lastname: Mugasimangalam
authors.affiliation: Department of Bioinformatics, QTLomics Technologies Pvt. Ltd Bangalore, India.
authors.forename: Nagesh A
authors.initials: NA
authors.lastname: Kuravadi
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center Bet-Dagan, Israel.
authors.forename: Bettina
authors.initials: B
authors.lastname: Kochanek
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center Bet-Dagan, Israel.
authors.forename: Shoshana
authors.initials: S
authors.lastname: Salim
authors.affiliation: Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Tucker
authors.affiliation: Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center Bet-Dagan, Israel.
authors.forename: Shimon
authors.initials: S
authors.lastname: Meir
keywords: RNA-Sequencing; auxin; ethylene; flower pedicel abscission; leaf petiole abscission; oligonucleotide microarray; tomato (Solanum lycopersicum); transcriptome
references.citation: Nature. 2001 Jan 25;409(6819):469-71
references.pmid: 11206529
references.citation: J Exp Bot. 2008;59(3):585-93
references.pmid: 18250077
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Science. 2005 Sep 2;309(5740):1559-63
references.pmid: 16141072
references.citation: Sci Rep. 2014 May 23;4:5054
references.pmid: 24852237
references.citation: Plant Mol Biol. 1996 Sep;31(6):1227-31
references.pmid: 8914538
references.citation: Plant J. 2009 May;58(4):641-54
references.pmid: 19175771
references.citation: BMC Genomics. 2014 Oct 13;15:892
references.pmid: 25308090
references.citation: Annu Rev Plant Biol. 2002;53:131-58
references.pmid: 12221970
references.citation: Gene. 2013 Aug 1;525(1):58-76
references.pmid: 23644021
references.citation: BMC Plant Biol. 2011 Oct 17;11:138
references.pmid: 22003957
references.citation: Mol Genet Genomics. 2012 Jun;287(6):495-513
references.pmid: 22570076
references.citation: J Exp Bot. 2008;59(4):973-9
references.pmid: 18316316
references.citation: Genetics. 1995 Mar;139(3):1393-409
references.pmid: 7768447
references.citation: J Exp Bot. 2005 Mar;56(413):817-23
references.pmid: 15689341
references.citation: Cell. 2009 Mar 20;136(6):1005-16
references.pmid: 19303845
references.citation: Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):1064-9
references.pmid: 11805344
references.citation: Plant Cell. 2005 Dec;17(12):3282-300
references.pmid: 16284307
references.citation: Bioinformatics. 2012 Apr 15;28(8):1086-92
references.pmid: 22368243
references.citation: Plant Physiol. 2006 Aug;141(4):1604-16
references.pmid: 16778017
references.citation: Plant Signal Behav. 2011 Apr;6(4):590-3
references.pmid: 21543890
references.citation: Development. 2009 Mar;136(5):823-32
references.pmid: 19176589
references.citation: J Exp Bot. 2007;58(12):3395-406
references.pmid: 17916637
references.citation: J Biol Chem. 1998 Oct 9;273(41):26631-7
references.pmid: 9756903
references.citation: Genome Res. 2008 Sep;18(9):1509-17
references.pmid: 18550803
references.citation: Cell Mol Life Sci. 1998 Jun;54(6):582-96
references.pmid: 9676577
references.citation: BMC Plant Biol. 2013 Mar 09;13:40
references.pmid: 23497084
references.citation: Development. 1995 Sep;121(9):2723-35
references.pmid: 7555701
references.citation: Genes Dev. 2008 Mar 15;22(6):810-23
references.pmid: 18347099
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9783-8
references.pmid: 10931949
references.citation: New Phytol. 2011 Aug;191(3):662-77
references.pmid: 21534969
references.citation: Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):290-5
references.pmid: 9874811
references.citation: Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11237-42
references.pmid: 14500916
references.citation: Plant Cell Physiol. 2002 Dec;43(12):1436-44
references.pmid: 12514240
references.citation: Plant Physiol. 2000 Jan;122(1):85-98
references.pmid: 10631252
references.citation: Nat Rev Genet. 2011 Feb;12(2):87-98
references.pmid: 21191423
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1114-7
references.pmid: 21097470
references.citation: PLoS One. 2013;8(3):e58363
references.pmid: 23484021
references.citation: Plant Physiol. 1997 Apr;113(4):1303-8
references.pmid: 9112778
references.citation: Annu Rev Genet. 2011;45:41-59
references.pmid: 22060040
references.citation: Plant Mol Biol. 1999 Nov;41(5):577-85
references.pmid: 10645718
references.citation: Ann Bot. 2005 Apr;95(5):707-35
references.pmid: 15749753
references.citation: Plant Mol Biol. 2003 Jul;52(4):801-15
references.pmid: 13677468
references.citation: Cereb Cortex. 2014 Jun;24(6):1451-9
references.pmid: 23377288
references.citation: Mol Genet Genomics. 2012 Mar;287(3):221-35
references.pmid: 22228229
references.citation: Plant Cell. 2011 Jul;23(7):2553-67
references.pmid: 21742991
references.citation: Mol Genet Genomics. 2011 Mar;285(3):245-60
references.pmid: 21290147
references.citation: Front Plant Sci. 2015 Dec 15;6:1109
references.pmid: 26697054
references.citation: Plant J. 2011 Jul;67(2):328-41
references.pmid: 21457372
references.citation: Nat Biotechnol. 2003 Apr;21(4):379-86
references.pmid: 12640466
references.citation: J Exp Bot. 2014 Jul;65(12):3111-9
references.pmid: 24744429
references.citation: Planta. 2006 Mar;223(4):646-58
references.pmid: 16200409
references.citation: Ann Bot. 2008 Jan;101(2):249-59
references.pmid: 17591611
references.citation: C R Biol. 2010 Apr;333(4):371-81
references.pmid: 20371112
references.citation: Plant Mol Biol. 1999 Jul;40(4):615-22
references.pmid: 10480385
references.citation: Science. 1995 May 5;268(5211):667-75
references.pmid: 7732375
references.citation: Annu Rev Genet. 2004;38:37-59
references.pmid: 15568971
references.citation: Plant Cell. 1995 Feb;7(2):173-82
references.pmid: 7756828
references.citation: Development. 2005 Oct;132(20):4563-74
references.pmid: 16176952
references.citation: J Exp Bot. 2002 Oct;53(377):2057-63
references.pmid: 12324529
references.citation: Plant Cell. 1997 Jul;9(7):1169-79
references.pmid: 9254934
references.citation: Nature. 1996 Jan 4;379(6560):66-9
references.pmid: 8538741
references.citation: Science. 1999 Jun 25;284(5423):2148-52
references.pmid: 10381874
references.citation: Cell. 1998 Dec 11;95(6):805-15
references.pmid: 9865698
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4908-12
references.pmid: 15781858
references.citation: BMC Genomics. 2015 Feb 05;16:39
references.pmid: 25652024
references.citation: BMC Genomics. 2010 Mar 16;11:180
references.pmid: 20233449
references.citation: Plant Physiol. 2008 Jul;147(3):1034-45
references.pmid: 18467465
references.citation: Gene. 2016 Feb 1;576(2 Pt 1):603-9
references.pmid: 26477480
references.citation: Trends Plant Sci. 2010 May;15(5):247-58
references.pmid: 20304701
references.citation: Genes Dev. 1998 Dec 1;12(23):3703-14
references.pmid: 9851977
references.citation: Plant J. 2007 Dec;52(5):865-76
references.pmid: 17883372
references.citation: J Exp Bot. 2008;59(10 ):2717-33
references.pmid: 18515267
references.citation: Nat Genet. 2006 Jun;38(6):626-35
references.pmid: 16645617
references.citation: Curr Opin Plant Biol. 2007 Oct;10(5):453-60
references.pmid: 17900969
references.citation: Ann Bot. 2008 Jan;101(2):285-92
references.pmid: 17965027
references.citation: BMC Genomics. 2009 Nov 24;10:555
references.pmid: 19930683
references.citation: Plant Cell. 2002 Dec;14(12):3163-76
references.pmid: 12468734
references.citation: Plant Physiol. 2004 Jun;135(2):660-7
references.pmid: 15208412
references.citation: Genome Res. 2005 Apr;15(4):463-74
references.pmid: 15781571
references.citation: Curr Biol. 2001 Dec 11;11(24):1914-22
references.pmid: 11747817
references.citation: Nature. 2009 May 28;459(7246):583-6
references.pmid: 19478783
references.citation: Science. 2006 Mar 31;311(5769):1936-9
references.pmid: 16527928
references.citation: Plant Physiol. 2008 Mar;146(3):1305-21
references.pmid: 18192438
references.citation: Annu Rev Biophys Biomol Struct. 1999;28:29-56
references.pmid: 10410794
references.citation: Science. 1998 May 15;280(5366):1091-4
references.pmid: 9582125
references.citation: J Mol Biol. 1993 Apr 20;230(4):1131-44
references.pmid: 8487298
references.citation: Plant Physiol. 1996 Jul;111(3):813-20
references.pmid: 8754682
references.citation: BMC Plant Biol. 2009 Oct 23;9:127
references.pmid: 19852773
references.citation: Nature. 2012 May 30;485(7400):635-41
references.pmid: 22660326
references.citation: Plant J. 2014 Jan;77(2):284-96
references.pmid: 24274099
references.citation: Planta. 1984 Feb;160(2):159-63
references.pmid: 24258418
references.citation: Plant Cell. 2000 Mar;12(3):393-404
references.pmid: 10715325
references.citation: Trends Genet. 2005 Feb;21(2):93-102
references.pmid: 15661355
references.citation: Plant Physiol. 2002 Nov;130(3):1487-96
references.pmid: 12428013
references.citation: BMC Genomics. 2015 Jan 22;16:9
references.pmid: 25612924
references.citation: Planta. 2010 Aug;232(3):755-64
references.pmid: 20571824
references.citation: PLoS One. 2014 Jul 18;9(7):e103032
references.pmid: 25036993
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Plant Cell Rep. 2011 Nov;30(11):2059-73
references.pmid: 21735233
references.citation: Curr Opin Biotechnol. 2011 Feb;22(1):32-41
references.pmid: 21074401
references.citation: Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5401-6
references.pmid: 9560288
references.citation: Annu Rev Cell Dev Biol. 2004;20:125-51
references.pmid: 15473837
references.citation: Physiol Plant. 2011 Feb;141(2):166-76
references.pmid: 21044084
references.citation: J Exp Bot. 2012 Oct;63(17):6079-91
references.pmid: 23028022
references.citation: Development. 2002 Jul;129(13):3195-206
references.pmid: 12070094
references.citation: Mol Genet Genomics. 2015 Dec;290(6):2089-105
references.pmid: 25982744
references.citation: Plant J. 2004 Oct;40(1):22-34
references.pmid: 15361138
references.citation: Plant J. 2003 Jan;33(2):221-33
references.pmid: 12535337
references.citation: Plant J. 2000 Mar;21(6):553-62
references.pmid: 10758506
references.citation: Chromosome Res. 2005;13(3):259-74
references.pmid: 15868420
references.citation: Plant Physiol. 2000 Jul;123(3):869-81
references.pmid: 10889236
references.citation: Plant Cell. 2009 Jan;21(1):216-33
references.pmid: 19168715
references.citation: J Exp Bot. 2011 Mar;62(6):1757-73
references.pmid: 21307383
references.citation: Plant J. 2012 May;70(4):585-98
references.pmid: 22211518
references.citation: BMC Genomics. 2013 Dec 09;14:866
references.pmid: 24320622
references.citation: Plant Physiol. 2012 Jan;158(1):439-50
references.pmid: 22106095
references.citation: PLoS One. 2013;8(2):e55238
references.pmid: 23390523
references.citation: Plant Sci. 2014 Dec;229:86-95
references.pmid: 25443836
references.citation: Mol Genet Genomics. 2012 Apr;287(4):295-11
references.pmid: 22314799
references.citation: Genomics. 2005 Jan;85(1):1-15
references.pmid: 15607417
references.citation: Cell. 1993 Feb 12;72(3):427-41
references.pmid: 8431946
references.citation: Gene. 2013 Aug 1;525(1):26-34
references.pmid: 23651590
references.citation: Science. 2006 Mar 31;311(5769):1886
references.pmid: 16574859
references.citation: Int J Mol Sci. 2012 Nov 29;13(12):16084-103
references.pmid: 23443112
references.citation: Plant Mol Biol. 1999 Apr;39(6):1073-8
references.pmid: 10380795
references.citation: Plant Cell. 1994 Oct;6(10):1485-93
references.pmid: 7994180
references.citation: Plant Cell Physiol. 2013 Feb;54(2):244-69
references.pmid: 23292600
references.citation: Plant J. 2001 Apr;26(1):47-58
references.pmid: 11359609
references.citation: Virology. 2015 Nov;485:305-12
references.pmid: 26319212
references.citation: Curr Opin Plant Biol. 2006 Feb;9(1):59-65
references.pmid: 16337172
references.citation: Development. 2009 Aug;136(16):2675-88
references.pmid: 19633168
references.citation: BMC Genomics. 2013 Jan 17;14:37
references.pmid: 23327667
references.citation: Plant Cell. 2004;16 Suppl:S170-80
references.pmid: 15010516
references.citation: Plant Physiol. 2015 Mar;167(3):844-53
references.pmid: 25560879
references.citation: Plant Physiol. 2011 Jan;155(1):185-208
references.pmid: 21037112
references.citation: Plant Cell. 2005 Feb;17(2):616-27
references.pmid: 15659623
references.citation: Nature. 2000 Aug 24;406(6798):910-3
references.pmid: 10972295
references.citation: Proc Natl Acad Sci U S A. 2009 May 19;106(20):8392-7
references.pmid: 19416824
references.citation: Curr Opin Plant Biol. 2001 Dec;4(6):527-32
references.pmid: 11641069
references.citation: CSH Protoc. 2008 Nov 01;2008:pdb.emo105
references.pmid: 21356708
references.citation: Science. 2000 Dec 15;290(5499):2105-10
references.pmid: 11118137
references.citation: Cold Spring Harb Protoc. 2011 Aug 01;2011(8):940-9
references.pmid: 21807852
references.citation: Plant Physiol. 2010 Dec;154(4):1929-56
references.pmid: 20947671