Variant Site Strain Typer (VaST): Efficient strain typing using a minimal number of variant genomic sites

This repository contains the matrices used to build the minimum spanning sets for <i>Yersenia pestis, Bacillus anthracis, </i><i>Escherichia</i><i> coli, Burkholderia pseudomallei, and Francisella tularensis. </i>The target sites identified for resolving each strain complex is also provided in the haplotype files. The loci used for the truncated, experimentally-validated panel are also listed. <br

Phylogenetic analysis of Grapevine redleaf-associated virus (GRLaV) using (A) coat protein and (B) replication-associated protein.

<p>Maximum likelihood trees were constructed using amino acid sequences of the coat protein (CP) and replication-associated protein (Rep) of GRLaV and representative members of approved genera in the family <i>Geminiviridae</i>. The consensus tree for each gene was drawn to scale using the MEGA5 with the rtREV amino acid substitution model and bootstrap values (1,000 replicates) shown at the nodes. Branches with less than 70% bootstrap support have been collapsed. Colored lines in both phylograms correspond to respective genera of the <i>Geminiviridae</i> family listed on the top left corner.</p

Graft transmission of grapevine redleaf disease (GRD) and associated viruses and viroids.

†<p>CF = Cabernet Franc, MR = Merlot.</p>*<p>Single-budded, virus-free scion of Cabernet Franc (CF).</p><p>GRLaV = Grapevine redleaf-associated virus, GRSPaV = <i>Grapevine rupestris stem pitting-associated virus</i>, GFLV = <i>Grapevine fanleaf virus</i>, HpSVd = <i>Hop stunt viroid</i>, GYSVd-1 = <i>Grapevine yellow speckle viroid 1</i>, GYSVd-2 = <i>Grapevine yellow speckle viroid 2</i>, CEVd = <i>Citrus exocortis viroid</i>, and CEYVd = <i>Citrus exocortis Yucatan viroid</i>.</p><p>Symptoms and the presence of Grapevine redleaf-associated virus and other viruses and viroids in Cabernet Franc scions grafted onto rootstocks of Merlot and Cabernet Franc with and without GRD symptoms.</p

A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family <i>Geminiviridae</i> Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing

<div><p>A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (<i>Vitis vinifera</i> L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and <i>Grapevine fanleaf virus</i> were detected only in grapevines showing GRD symptoms. In contrast, <i>Grapevine rupestris stem pitting-associated virus</i>, <i>Hop stunt viroid</i>, <i>Grapevine yellow speckle viroid 1</i>, <i>Citrus exocortis viroid</i> and <i>Citrus exocortis Yucatan viroid</i> were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (<i>Erythroneura ziczac</i> Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family <i>Geminiviridae</i> with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.</p></div

Detection of Grapevine redleaf-associated virus (GRLaV) and <b><i>Grapevine leafroll-associated virus 3</i></b><b> (GLRaV-3) in Virginia creeper leafhopper exposed to grapevines mixed infected with GRLaV and GLRaV-3.</b>

<p>An agarose gel (0.8%) showing (A) amplification of partial IR and CP regions of GRLaV and (B) no amplification of GLRaV-3-specific sequence from individual leafhoppers (lanes 1–6) subjected to 72 hr acquisition access on Mourvèdre mixed infected with GRLaV and GLRaV-3. ‘+’ represents positive control for the respective viruses, ‘−’ represents healthy control negative for the respective viruses, and ‘M’ represents 1 kb plus DNA ladder (Invitrogen). Arrow represents ∼550 bp and ∼330 bp DNA band specific to GRLaV (A) and GLRaV-3 (B), respectively.</p

Field symptoms of grapevine redleaf disease in two red-berried wine grape cultivars.

<p>(A) Merlot grapevine with symptoms on the left and non-symptomatic grapevine on the right. (B) and (C) Leaves of Merlot showing red veins and irregular blotches in the initial and advanced stages of symptom development, respectively, are on the left and leaves from non-symptomatic grapevines on the right. (D) Cabernet Franc grapevine with symptoms on the right and non-symptomatic grapevine on the left. (E) and (F) Leaves of Cabernet Franc showing discolorations between veins in the early and advanced stages of symptom development, respectively, are on the right and leaves from non-symptomatic grapevines on the left. Symptomatic leaves of GRD-affected grapevines are smaller in size compared to leaves from neighboring non-symptomatic grapevines. Note differences in color of symptomatic leaves between the two cultivars and red veins in Merlot (B–C) and presence of a narrow strip of green tissue on either side of the major veins (green veins) in Cabernet Franc (E–F).</p

Impacts of Grapevine redleaf disease (GRD) on yield and berry quality parameters for Merlot grapevines.

<p>Impacts of the disease on (A) shoot length, (B) fruit yield, (C) number of clusters, (D) pruning weight, (E) leaf carbohydrates, and (F) total soluble solids, (G) anthocyanins, (H) titratable acidity and (I) pH of berries from symptomatic (red color columns) and non-symptomatic (green color columns) grapevines. Columns represent mean value and vertical bars indicate standard errors. Significant differences between symptomatic and non-symptomatic grapevines was determined by one-way ANOVA using the SigmaPlot 11 software and indicated by asterisks (* = p≤0.05 and ** = p≤0.001).</p

Impacts of Grapevine redleaf disease (GRD) on yield and berry quality parameters for Cabernet Franc grapevines.

<p>Impacts of the disease on (A) shoot length, (B) fruit yield, (C) number of clusters, (D) pruning weight, (E) leaf carbohydrates, and (F) total soluble solids, (G) anthocyanins, (H) titratable acidity and (I) pH of berries from symptomatic (red color columns) and non-symptomatic (green color columns) grapevines. Columns represent mean value and vertical bars indicate standard errors. Significant differences between symptomatic and non-symptomatic grapevines was determined by one-way ANOVA using the SigmaPlot 11 software and indicated by asterisks (* = p≤0.05 and ** = p≤0.001).</p

Virginia creeper leafhopper (<i>Erythroneura ziczac</i> Walsh) on grapevine leaves.

<p>Adult leafhoppers and their feeding damage on the adaxial surface of a grapevine leaf. The inset is a close-up of an adult leafhopper showing reddish-brown eyes, pale yellow to light brownish-yellow body color and a more regular reddish-brown zigzag pattern on the wings.</p

Detection of Grapevine redleaf-associated virus (GRLaV) in grapevines inoculated with viruliferous Virginia creeper leafhoppers.

<p>An agarose gel (0.8%) showing amplification of partial IR and CP regions of GRLaV from (A) Cabernet Franc, (B) Chardonnay, (C) Merlot, (D) Pinot Noir, (E) Pixie and (F) Sangiovese. Lanes 1 to 5 represent individual grapevines, ‘+’ represents positive control for GRLaV, ‘−’ represents healthy control negative for GRLaV, and ‘M’ represents 1 kb plus DNA ladder (Invitrogen). Arrows represent ∼550 bp DNA band specific to GRLaV.</p