title: Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera.
abstract: BACKGROUND
  WRKY transcription factors are one of the largest families of transcriptional regulators in plants. WRKY genes are not only found to play significant roles in biotic and abiotic stress response, but also regulate growth and development. Grapevine (Vitis vinifera) production is largely limited by stressful climate conditions such as cold stress and the role of WRKY genes in the survival of grapevine under these conditions remains unknown.
  
  
  RESULTS
  We identified a total of 59 VvWRKYs from the V. vinifera genome, belonging to four subgroups according to conserved WRKY domains and zinc-finger structure. The majority of VvWRKYs were expressed in more than one tissue among the 7 tissues examined which included young leaves, mature leaves, tendril, stem apex, root, young fruits and ripe fruits. Publicly available microarray data suggested that a subset of VvWRKYs was activated in response to diverse stresses. Quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 36 VvWRKYs are changed following cold exposure. Comparative analysis was performed on data from publicly available microarray experiments, previous global transcriptome analysis studies, and qRT-PCR. We identified 15 VvWRKYs in at least two of these databases which may relate to cold stress. Among them, the transcription of three genes can be induced by exogenous ABA application, suggesting that they can be involved in an ABA-dependent signaling pathway in response to cold stress.
  
  
  CONCLUSIONS
  We identified 59 VvWRKYs from the V. vinifera genome and 15 of them showed cold stress-induced expression patterns. These genes represented candidate genes for future functional analysis of VvWRKYs involved in the low temperature-related signal pathways in grape.
authors.forename: Lina
authors.initials: L
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.forename: Linchuan
authors.initials: L
authors.lastname: Fang
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Sun
authors.forename: Lingye
authors.initials: L
authors.lastname: Su
authors.forename: Zhenchang
authors.initials: Z
authors.lastname: Liang
authors.forename: Nian
authors.initials: N
authors.lastname: Wang
authors.forename: Jason P
authors.initials: JP
authors.lastname: Londo
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China. shhli@wbgcas.cn.
authors.forename: Shaohua
authors.initials: S
authors.lastname: Li
authors.forename: Haiping
authors.initials: H
authors.lastname: Xin
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D000595:Amino Acid Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D003080:Cold Temperature; D017124:Conserved Sequence / Q000235:genetics; D003433:Crosses, Genetic; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics*; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D027843:Vitis / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors; D000040:Abscisic Acid
references.citation: Trends Plant Sci. 2001 Jun;6(6):262-7
references.pmid: 11378468
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D1152-8
references.pmid: 23180799
references.citation: Mol Plant Pathol. 2013 Feb;14(2):131-44
references.pmid: 23057972
references.citation: Genome Biol. 2007;8(2):R19
references.pmid: 17291332
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Mol Biol Rep. 2012 Apr;39(4):4553-64
references.pmid: 21938429
references.citation: BMC Genomics. 2012 Jun 22;13:270
references.pmid: 22726208
references.citation: Plant J. 2008 Dec;56(6):935-47
references.pmid: 18702671
references.citation: Nucleic Acids Res. 2009 Apr;37(6):e45
references.pmid: 19237396
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1194-201
references.pmid: 22084198
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507
references.citation: Plant Mol Biol. 2011 Oct;77(3):261-74
references.pmid: 21786204
references.citation: Biochim Biophys Acta. 2008 Nov;1779(11):780-8
references.pmid: 18471443
references.citation: Plant Physiol. 2005 Jan;137(1):176-89
references.pmid: 15618416
references.citation: Mol Gen Genet. 1994 Sep 28;244(6):563-71
references.pmid: 7969025
references.citation: Mol Plant Microbe Interact. 2003 Apr;16(4):295-305
references.pmid: 12744458
references.citation: FEBS Lett. 2005 Feb 28;579(6):1545-50
references.pmid: 15733871
references.citation: Plant Mol Biol. 2010 Jan;72(1-2):215-34
references.pmid: 19902151
references.citation: Mol Biol Rep. 2011 Aug;38(6):4023-35
references.pmid: 21110110
references.citation: Mol Plant Microbe Interact. 2006 Oct;19(10):1103-12
references.pmid: 17022174
references.citation: Curr Opin Plant Biol. 2004 Oct;7(5):491-8
references.pmid: 15337090
references.citation: PLoS One. 2013;8(3):e58740
references.pmid: 23516547
references.citation: Plant Biotechnol J. 2007 Jan;5(1):192-206
references.pmid: 17207268
references.citation: BMC Plant Biol. 2006 Nov 14;6:27
references.pmid: 17105665
references.citation: Physiol Plant. 2007 Nov;131(3):434-47
references.pmid: 18251882
references.citation: Plant Physiol. 2004 Mar;134(3):1006-16
references.pmid: 14976236
references.citation: BMC Plant Biol. 2012 Aug 12;12:144
references.pmid: 22883108
references.citation: J Exp Bot. 2007;58(8):1999-2010
references.pmid: 17456504
references.citation: Plant Mol Biol. 2012 Oct;80(3):241-53
references.pmid: 22875749
references.citation: DNA Res. 2012 Apr;19(2):153-64
references.pmid: 22279089
references.citation: Plant Cell Rep. 2012 Nov;31(11):2109-20
references.pmid: 22847334
references.citation: Plant Mol Biol. 1995 Nov;29(4):691-702
references.pmid: 8541496
references.citation: Plant Mol Biol. 2002 Mar;48(4):339-50
references.pmid: 11905961
references.citation: BMC Evol Biol. 2005 Jan 03;5:1
references.pmid: 15629062
references.citation: BMC Genomics. 2011 Sep 28;12:471
references.pmid: 21955985
references.citation: Planta. 2010 Nov;232(6):1325-37
references.pmid: 20811906
references.citation: Mol Plant. 2012 Nov;5(6):1375-88
references.pmid: 22930734
references.citation: Trends Plant Sci. 2000 May;5(5):199-206
references.pmid: 10785665
references.citation: Planta. 2009 Nov;230(6):1155-66
references.pmid: 19760263
references.citation: EMBO J. 1996 Oct 15;15(20):5690-700
references.pmid: 8896462
references.citation: Gene. 2012 Jul 25;503(2):248-53
references.pmid: 22579867
references.citation: Plant Biotechnol J. 2012 Jan;10(1):2-11
references.pmid: 21696534
references.citation: Plant Physiol. 2009 Oct;151(2):936-48
references.pmid: 19700558
references.citation: Bioinformatics. 2006 Jan 15;22(2):195-201
references.pmid: 16301204
references.citation: EMBO J. 1999 Sep 1;18(17):4689-99
references.pmid: 10469648
references.citation: J Exp Bot. 2010 Sep;61(14):3901-14
references.pmid: 20643804
references.citation: Plant Mol Biol. 2009 Jan;69(1-2):91-105
references.pmid: 18839316
references.citation: Mol Biol Rep. 2011 Jan;38(1):417-27
references.pmid: 20354906
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Plant Physiol. 2004 Jun;135(2):615-21
references.pmid: 15173567
references.citation: Funct Integr Genomics. 2007 Apr;7(2):111-34
references.pmid: 17136344
references.citation: Plant J. 2010 Aug;63(3):417-29
references.pmid: 20487379
references.citation: DNA Res. 2005 Feb 28;12(1):9-26
references.pmid: 16106749
references.citation: Trends Plant Sci. 2010 May;15(5):247-58
references.pmid: 20304701
references.citation: Funct Integr Genomics. 2010 Aug;10(3):367-81
references.pmid: 19841954
references.citation: Biochim Biophys Acta. 2004 Sep 17;1679(3):279-87
references.pmid: 15358520
references.citation: Funct Integr Genomics. 2007 Oct;7(4):317-33
references.pmid: 17578611
references.citation: Planta. 2011 Sep;234(3):541-54
references.pmid: 21547461
references.citation: Plant Sci. 2011 Jan;180(1):3-11
references.pmid: 21421341
references.citation: Plant Mol Biol. 2004 May;55(3):399-416
references.pmid: 15604689
references.citation: Funct Integr Genomics. 2007 Apr;7(2):95-110
references.pmid: 16775684
references.citation: Plant Cell Rep. 2009 Jan;28(1):21-30
references.pmid: 18818929
references.citation: Plant Physiol. 2008 Jan;146(1):236-49
references.pmid: 17993546
references.citation: New Phytol. 2013 Nov;200(3):834-846
references.pmid: 23905547
references.citation: Funct Integr Genomics. 2012 Mar;12(1):183-98
references.pmid: 21811781