Grape <i>TIFY</i> genes.

<p>Grape <i>TIFY</i> genes.</p

Phylogenetic analysis of grape, <i>Arabidopsis</i> and rice TIFY proteins.

<p>Phylogenetic tree was constructed with TIFY protein sequences from <i>V. vinifera</i> (Vv), <i>O. sativa</i> (Os) and <i>A. thaliana</i> (Ath).</p

Distribution and synteny of <i>ZML</i>, <i>PPD</i> and <i>JAZ</i>

<p><b>genes on grape chromosomes.</b> Chromosomes 1–19 (chr1–19) are depicted as horizontal gray bars. <i>ZML</i>, <i>PPD</i> and <i>JAZ</i> genes are indicated by vertical orange lines. Colored bars denote syntenic regions of the grape genome; a twisted colored bar indicates that syntenic regions are in opposite orientations.</p

Expression levels of <i>TIFY</i> genes and <i>VvCOI1</i> following Eth treatment in the leaves of Chinese wild <i>Vitis pseudoreticulata</i> ‘Hunan-1’.

<p>Grape <i>Actin1</i> was used as internal control for qRT-PCR and fold changes indicate expression level in treated leaves compared with negative control, which was set to 1. Mean values and SDs were obtained from three technical and three biological replicates.</p

Hierarchical clustering of a selection of <i>TIFY</i> genes.

<p>Details of the experimental conditions are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044465#pone.0044465.s001" target="_blank">Table S1</a>. Log2 based fold-changes were used to create the heatmap. Differences in gene expression changes are shown in color as per the lower scale.</p

The ZML, PPD and JAZ protein subfamilies in grape.

<p>(A) Phylogenetic analysis of grape ZML, PPD and JAZ proteins. Numbers above or below branches of the tree indicate bootstrap values. (B) Exon/intron structures of grape <i>ZML, PPD</i> and <i>JAZ</i> genes. Only the exons, represented by green boxes, are drawn to scale. Black lines connecting two exons represent introns. (C) The distribution of conserved domains within grape ZML, PPD and JAZ proteins. The relative positions of each conserved domain within each protein are shown in color. (D) Sequence logo of the TIFY (D) and Jas (E) domains from grape TIFY proteins.</p

Synteny analysis of <i>ZML</i>, <i>PPD</i> and <i>JAZ</i> genes between grape and <i>Arabidopsis</i>.

<p>Grape and <i>Arabidopsis</i> chromosomes are depicted as horizontal gray and blue bars, respectively. Grape and <i>Arabidopsis TIFY</i> genes are indicated by vertical orange and blue lines, respectively. Colored bars denote syntenic regions between grape and <i>Arabidopsis</i> chromosomes; a twisted colored bar indicates that the syntenic regions are in opposite orientations.</p

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> </div

Identification of Tomato necrotic stunt virus (ToNSV) in the Mexican sample (MX) and its relationship with other viruses in the family of Potyviridae.

<p>A. Relative placement of <i>de novo</i> assembled siRNA contigs onto a general potyvirus genome. B. Distribution of siRNAs along the ToNSV genome in both (+) and (−) polarities. C. Phylogenetic relationship of the newly identified ToNSV genome in relationship to other viruses in the family of Potyviridae. The full name of potyviruses and their respective GenBank accession numbers are: ToNSV-MX9354: JQ314463; PTMV, <i>Peru tomato mosaic virus</i>: AJ516010; PVY-O, <i>Potato virus Y</i>: HQ912914; PeSMV, <i>Pepper severe mosaic virus</i>: AM181350; PeMoV, <i>Pepper mottle virus</i>: EU586135; PVV, Potato virus V: NC_004010; PepYMV, <i>Pepper yellow mosaic virus</i>: NC_014327; BiMoV, <i>Bidens mottle virus</i>: EU250214; WMV, <i>Watermelon mosaic virus</i>: DQ399708; PVMV, <i>Pepper veinal mottle virus</i>: FM202327; TVBMV, <i>Tobacco vein-banding mosaic virus</i>: EF219408; TVMV, <i>Tobacco vein mottling virus</i>: X04083; and TEV, <i>Tobacco etch virus</i>: EF470242. SPMMV, <i>Sweet potato mild mottle virus</i>: NC_003739, genus <i>Ipomovirus</i>, was used as an outgroup sequence to anchor the phylogenetic tree.</p

Počítačová podpora pro vzdálenou správu naměřených dat reálných úloh

Import 20/04/2006Prezenční výpůjčkaVŠB - Technická univerzita Ostrava. Fakulta strojní. Katedra (352) automatizační techniky a řízen