Genome-Wide Identification and Analysis of the <em>TIFY</em> Gene Family in Grape

<div><h3>Background</h3><p>The <em>TIFY</em> 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 <em>Arabidopsis</em> and rice that <em>TIFY</em> genes, and especially <em>JAZ</em> 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 <em>TIFY</em> family members is limited, especially in a woody species such as grape.</p> <h3>Methodology/Principal Findings</h3><p>A total of two <em>TIFY</em>, four <em>ZML</em>, two <em>PPD</em> and 11 <em>JAZ</em> genes were identified in the <em>Vitis vinifera</em> genome. Phylogenetic analysis of TIFY protein sequences from grape, <em>Arabidopsis</em> and rice indicated that the grape TIFY proteins are more closely related to those of <em>Arabidopsis</em> than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape <em>TIFY</em> family. In addition, synteny analysis between grape and <em>Arabidopsis</em> demonstrated that homologues of several grape <em>TIFY</em> genes were found in the corresponding syntenic blocks of <em>Arabidopsis</em>, suggesting that these genes arose before the divergence of lineages that led to grape and <em>Arabidopsis</em>. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape <em>TIFY</em> 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.</p> <h3>Conclusion</h3><p>The genome-wide identification, evolutionary and expression analyses of grape <em>TIFY</em> genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.</p>