title: Genome-wide identification and analysis of the TIFY gene family in grape.
abstract: BACKGROUND
  The TIFY gene family constitutes a plant-specific group of genes with a broad range of functions. This family encodes four subfamilies of proteins, including ZML, TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. JAZ proteins are targets of the SCF(COI1) complex, and function as negative regulators in the JA signaling pathway. Recently, it has been reported in both Arabidopsis and rice that TIFY genes, and especially JAZ genes, may be involved in plant defense against insect feeding, wounding, pathogens and abiotic stresses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape.
  
  
  RESULTS
  A total of two TIFY, four ZML, two PPD and 11 JAZ genes were identified in the Vitis vinifera genome. Phylogenetic analysis of TIFY protein sequences from grape, Arabidopsis and rice indicated that the grape TIFY proteins are more closely related to those of Arabidopsis than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape TIFY family. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologues of several grape TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape TIFY genes are not a major player in the defense against biotrophic pathogens or viruses. However, many of these genes were responsive to JA and ABA, but not SA or ET.
  
  
  CONCLUSIONS
  The genome-wide identification, evolutionary and expression analyses of grape TIFY genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.
authors.affiliation: College of Horticulture, Northwest A&F University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, PR China.
authors.forename: Yucheng
authors.initials: Y
authors.lastname: Zhang
authors.forename: Min
authors.initials: M
authors.lastname: Gao
authors.forename: Stacy D
authors.initials: SD
authors.lastname: Singer
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: Hua
authors.initials: H
authors.lastname: Wang
authors.forename: Xiping
authors.initials: X
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D016000:Cluster Analysis; D005091:Exons; D050980:GATA Transcription Factors / Q000235:genetics*; D055106:Genome-Wide Association Study; D007438:Introns; D008390:Markov Chains; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D018521:Plant Physiological Phenomena; D010940:Plant Proteins / Q000235:genetics; D027843:Vitis / Q000235:genetics* / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins; D050980:GATA Transcription Factors; D010940:Plant Proteins; C578310:ZML1 protein, Arabidopsis