Australian grapevine viroid--evidence for extensive recombination between viroids.

Australian grapevine viroid (AGV, 369 residues) is a novel viroid with less than 50% sequence similarity with any known viroid. Nevertheless its entire sequence can be divided into regions, each with a high sequence similarity with segments from one of citrus exocortis, potato spindle tuber, apple scar skin, and grapevine yellow speckle viroids. AGV contains the entire central conserved region of the apple scar skin viroid group and is proposed as a member of this group. AGV appears to have originated from extensive RNA recombination involving other viroids. The vegetatively propagated grapevines which have been exposed to multiple viroid infections during their long history of cultivation may have allowed such recombination.     

Incidence of Viruses and Nematode Vectors in Lebanese Vineyards

Surveys for virus diseases and nematode vectors were conducted in 95 commercial vineyards of four different Lebanese districts (Bekaa valley, Mount Lebanon, North and South Lebanon). Out of 915 randomly collected grapevine samples tested by ELISA, 511 (55.8%) were infected by one or more viruses. Grapevine virus A (30.9%) and Grapevine leafroll‐associated virus 3 (23.7%) were the prevailing viruses, followed by Grapevine fleck virus (15.1%), Grapevine leafroll‐associated virus 1 (10.6%) and Grapevine leafroll‐associated virus 2 (8.7%). Arabis mosaic virus was not found whereas Grapevine fanleaf virus (GFLV) and Grapevine virus B were little represented. The most important Lebanese grapevine varieties, i.e. Maghdouchi, Tfeifihi and Beitamouni, had average infection rates between 70% and 87%, whereas varieties of foreign origin had a better sanitary status with the exception of cvs Cinsaut and Thompson (c. 83% infection). Grapevine rupestris stem pitting‐associated virus was detected in 79 of 90 (87.8%) samples tested by RT‐PCR and closteroviruses were recorded in seven of 70 (10%) vines tested. One of these viruses was identified as Grapevine leafroll‐associated virus 5 by ELISA and partial genome sequencing. No nepoviruses other than GFLV were detected in any of 90 samples tested using three different sets of degenerate primers. Xiphinema index was found in 23 of 89 soil samples collected from vineyards, and in three of 15 samples collected primarily under fig trees in fields where no grapevines were grown.     

Modulation of flavonoid biosynthetic pathway genes and anthocyanins due to virus infection in grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis>L.) leaves

Background  

Symptoms of grapevine leafroll disease (GLRD) in red-fruited wine grape (Vitis vinifera L.) cultivars consist of green veins and red and reddish-purple discoloration of inter-veinal areas of leaves. The reddish-purple color of symptomatic leaves may be due to the accumulation of anthocyanins and could reflect an up-regulation of genes involved in their biosynthesis.     

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

A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera 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 Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac 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 Geminiviridae 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.     

Grapevine yellow speckle viroid: structural features of a new viroid group.

A single stranded circular RNA was isolated from grapevines infected with yellow speckle disease. The RNA which we have called grapevine yellow speckle viroid (GYSV), contains 367 nucleotide residues and has the potential to form the rod-like secondary structure characteristic of viroids. GYSV has 37% sequence homology with the recently described apple scar skin viroid (ASSV; 330 residues) and has some sequence homology with the viroids in the potato spindle tuber viroid (PSTV) group. The sequence of GYSV has characteristics which fit the structural domains described for the PSTV group. However, GYSV lacks the PSTV central conserved sequence. Instead, there is a conserved sequence in the central region of GYSV and ASSV which has the potential to form a stem loop configuration and a stable palindromic structure as does the central conserved region of the PSTV group. These structural features suggest there is a different central conserved region for GYSV and ASSV. The results support the viroid nature of GYSV and its inclusion into a separate viroid group which we suggest should be represented by ASSV.     

Evaluation of biological indexing and dsRNA analysis in grapevine virus elimination

Fragmented shoot apex culture (FSAC) was used to eliminate some diseases caused by viruses and virus-like agents from 24 varieties of imported grapevines. Each cultivar was examined by biological indexing before and after FSAC. Graft indexing revealed that leaf roll, stem pitting and yellow speckle diseases were common before FSAC. A correlation was observed between the incidence of leafroll disease and the presence of specific dsRNA species which were removed after FSAC. One of these species, an RNA of about one kilobase pair was associated with low yielding Sultana clones. Both biological indexing and dsRNA assay indicated no recurrence of the leafroll disease in material regenerated by FSAC even after 10 years in the field. It is concluded that dsRNA assay may be used as a faster and less expensive method than biological indexing in assessing the success of leafroll elimination by FSAC. The test also provides some information on the genome size of the viruses associated with leafroll disease. Graft indexing indicated that yellow speckle disease was resistant to elimination by FSAC, while stem pitting was removed from some of the vines and the grapevine fleck disease was eliminated from most sources.     

Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction

Background

Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21–24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms.

Methodology/Principal Findings

To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1) were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots) of the genomic (+) and (−) viroid RNAs, with a prevalence of those from the (−) strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots.

Conclusions/Significance

These findings show that different Dicer-like enzymes (DCLs) target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression.     

Localization and subcellular association of Grapevine Pinot Gris Virus in grapevine leaf tissues

Despite the increasing impact of Grapevine Pinot gris disease (GPG-disease) worldwide, etiology about this disorder is still uncertain. The presence of the putative causal agent, the Grapevine Pinot Gris Virus (GPGV), has been reported in symptomatic grapevines (presenting stunting, chlorotic mottling, and leaf deformation) as well as in symptom-free plants. Moreover, information on virus localization in grapevine tissues and virus-plant interactions at the cytological level is missing at all. Ultrastructural and cytochemical investigations were undertaken to detect virus particles and the associated cytopathic effects in field-grown grapevine showing different symptom severity. Asymptomatic greenhouse-grown grapevines, which tested negative for GPGV by real time RT-PCR, were sampled as controls. Multiplex real-time RT-PCR and ELISA tests excluded the presence of viruses included in the Italian certification program both in field-grown and greenhouse-grown grapevines. Conversely, evidence was found for ubiquitous presence of Grapevine Rupestris Stem Pitting-associated Virus (GRSPaV), Hop Stunt Viroid (HSVd), and Grapevine Yellow Speckle Viroid 1 (GYSVd-1) in both plant groups. Moreover, in every field-grown grapevine, GPGV was detected by real-time RT-PCR. Ultrastructural observations and immunogold labelling assays showed filamentous flexuous viruses in the bundle sheath cells, often located inside membrane-bound organelles. No cytological differences were observed among field-grown grapevine samples showing different symptom severity. GPGV localization and associated ultrastructural modifications are reported and discussed, in the perspective of assisting management and control of the disease.     

Detection of Grapevine Viruses in Poland

During a 3‐year study, grapevines from 23 vineyards in Poland were surveyed for virus diseases and tested to determine the prevalence of the most economically important viruses by RT‐PCR. The rate of positive samples was 2.2% for grapevine leafroll‐associated virus 1 (GLRaV‐1), 1.9% for grapevine leafroll‐associated virus 2 (GLRaV‐2), 1.5% grapevine leafroll‐associated virus 3 (GLRaV‐3), 1.9% for grapevine virus A (GVA), 0.2% for grapevine virus B (GVB), 0.2% for grapevine virus E (GVE), 0.65% for grapevine fanleaf virus (GFLV), 20.4% for grapevine fleck virus (GFkV) and 71.9% for grapevine rupestris stem pitting‐associated virus (GRSPaV). These viruses were found to occur as single or mixed infections of different combinations in individual grapevines. The overall viral infection rate in the surveyed grapevines was 82.6%. GRSPaV is the most widely distributed virus of all the viruses currently detected in the region. DNA sequencing confirmed the identification of the viruses in selected samples, and analysis indicated that the Polish isolates shared a close molecular identity with the corresponding isolates in GenBank. To our knowledge, this is the first detection of GLRaV‐1, ‐2, ‐3, GVA, GVB, GVE, GFLV, GFkV and GRSPaV in Poland.     

Grapevine Viruses' Detection and Sanitary Selection in Grapevine Germplasm of Calabria (Southern Italy)

A survey of grapevine viruses present in the region of Calabria (southern Italy) was carried out, and the sanitary selection was conducted on various indigenous varieties. Serological (ELISA) and molecular (multiplex RT‐PCR) tests were used to detect the viruses included in the Italian certification programme: Arabis mosaic virus (ArMV), Grapevine fanleaf virus (GFLV), Grapevine leafroll associated virus 1 (GLRaV‐1), Grapevine leafroll associated virus 2 (GLRaV‐2), Grapevine leafroll associated virus 3 (GLRaV‐3), Grapevine virus A (GVA), Grapevine virus B (GVB) and Grapevine fleck virus (GFkV). The frequency with which the above viruses have been detected was 37.4, 32.6, 12.8, 7.7, 7.3, 1.9 and 0.3%, respectively, for GVA, GLRaV‐3, GFLV, GFKV, GLRaV‐1, GLRaV‐2 and GVB. ArMV was never found. The sanitary selection allowed for the detection of 6 putative clones of ‘Arvino’, 2 of ‘Magliocco dolce’ and 2 of the rootstock ‘17–37’ free of the above‐mentioned viruses. The necessary process for the commercialization of these clones as ‘certified’ propagation material was accomplished, and their official approval by the Italian Ministry of Agriculture is currently in progress.     

Transmission of Grapevine virus A and Grapevine leafroll‐associated viruses 1 and 3 by Planococcus ficus and Planococcus citri fed on mixed‐infected plants

The Grapevine virus A (GVA) and Grapevine leafroll‐associated viruses 1 and 3 (GLRaV‐1 and GLRaV‐3) are associated with grapevine diseases that induce severe reductions in yield and berry quality. These three viruses are known to coexist in both grapevine and insect vectors, but their cotransmission has been poorly characterised so far. This study investigates the acquisition and transmission of GLRaV‐1, GLRaV‐3 and GVA by Planococcus ficus and Planococcus citri (Hemiptera: Pseudococcidae) following feeding on multiple‐infected plants. The retention and load of the three viruses in the two insect species were analysed. After feeding onto GVA, GLRaV‐1 and GLRaV‐3 mixed‐infected grapevines, nymphs of P. ficus and P. citri showed similar virus acquisition rates and retained low quantities of viruses until the third post‐acquisition day. Despite the similar acquisition patterns, the two vectors differed in transmission efficiency: P. ficus showed a higher efficiency in transmitting GVA and GLRaV‐3, whereas P. citri transmitted GLRaV‐1 more efficiently. When focusing on the virus cotransmission, it appears that GVA could be transmitted to grapevine without GLRaV‐1 and/or GLRaV‐3 and that the transmission of both GLRaVs could take place in the absence of GVA. This comparative study involving different viruses and vector species improves the current knowledge of the semi‐persistent transmission of these three viruses and contributes to the understanding of grapevine virus epidemiology.     

Cultivated Grapevines Represent a Symptomless Reservoir for the Transmission of Hop Stunt Viroid to Hop Crops: 15 Years of Evolutionary Analysis

Hop stunt was a mysterious disorder that first emerged in the 1940s in commercial hops in Japan. To investigate the origin of this disorder, we infected hops with natural Hop stunt viroid (HpSVd) isolates derived from four host species (hop, grapevine, plum and citrus), which except for hop represent possible sources of the ancestral viroid. These plants were maintained for 15 years, then analyzed the HpSVd variants present. Here we show that the variant originally found in cultivated grapevines gave rise to various combinations of mutations at positions 25, 26, 54, 193, and 281. However, upon prolonged infection, these variants underwent convergent evolution resulting in a limited number of adapted mutants. Some of them showed nucleotide sequences identical to those currently responsible for hop stunt epidemics in commercial hops in Japan, China, and the United States. Therefore, these results indicate that we have successfully reproduced the original process by which a natural HpSVd variant naturally introduced into cultivated hops was able to mutate into the HpSVd variants that are currently present in commercial hops. Furthermore, and importantly, we have identified cultivated grapevines as a symptomless reservoir in which HSVd can evolve and be transmitted to hop crops to cause epidemics.     

Occurrence and Distribution of Grapevine Leafroll-associated Viruses 1, 2, 3 and 7 in Turkey

Grapevines in central Anatolia region of Turkey were surveyed for the prevalence of grapevine leafroll viruses. The field study and collection of samples were conducted in nine major grapevine‐growing areas. Samples collected from 622 vines were tested for Grapevine leafroll‐associated virus 1, 2, 3 and 7 (GLRaV‐1, ‐2, ‐3 and ‐7). According to diagnostic tests and surveys, 27 of 41 cultivars and 95 of 622 samples (15.27%) were found to be infected at least one virus. GLRaV‐1 (8.36%) was found to be the most frequently encountered virus associated with leafroll disease of grapes, followed by GLRaV‐3 (5.78%), GLRAV‐7 (3.86%) and GLRAV‐2 (2.41%).     

Truncatella angustata associated with grapevine trunk disease in northern Iran

In recent years, grapevine trunk diseases have gained growing attentions due to worldwide incidence of the disease. In a survey on fungal agents associated with grapevine trunk diseases in northern Iran, wood samples were collected from grapevines having the symptoms of declination. Isolation was made using routine plant pathology methods. A coelomycetous fungus with appendage-bearing conidia was recovered from symptomatic tissues. Based on morphological and cultural characteristics, the causal agent of the disease was identified as Truncatella angustata. The identity of the species was further confirmed by sequence data of internal transcribed spacer-rDNA region. A phylogeny inferred using sequence data obtained in this study, together with the sequences from GenBank, clustered our isolates together with T. angustata known from other host plant species. Pathogenicity tests performed on detached shoots of grapevines led to the same symptoms as observed in field conditions. This is first study on the pathogenicity of T. angustata on grapevine in Iran and first report on the occurrence of T. angustata on grapevine in Iran.     

Regeneration of virus-free grapevines using in vitro apical culture

Fragmented shoot apex culture of grapevine has been demonstrated to regenerate plants free from the graft-transmissible diseases leafroll, yellow speckle, fleck and summer mottle. This technique in combination with heat therapy of the cultures has also produced vines free from fanleaf virus. Regenerated plants free of yellow speckle were consistently obtained if cultures were incubated at 27/20 °C but not if incubated at 35 °C. The possible ways that the in vitro elimination of these diseases was achieved are considered.     

Major changes in grapevine wood microbiota are associated with the onset of esca,a devastating trunk disease

Esca, a major grapevine trunk disease in old grapevines, is associated with the colonization of woody tissues by a broad range of plant pathogenic fungi. To identify which fungal and bacterial species are involved in the onset of this disease, we analysed the microbiota from woody tissues of young (10-year-old) grapevines at an early stage of esca. Using meta-barcoding, 515 fungal and 403 bacterial operational taxonomic units (OTUs) were identified in woody tissues. In situ hybridization showed that these fungi and bacteria co-inhabited in grapevine woody tissues. In non-necrotic woody tissues, fungal and bacterial microbiota varied according to organs and seasons but not diseased plant status. Phaeomoniella chlamydospora, involved in the Grapevine trunk disease, was the most abundant species in non-necrotic tissues from healthy plants, suggesting a possible non-pathogenic endophytic behaviour. Most diseased plants (70%) displayed cordons, with their central white-rot necrosis colonized essentially by two plant pathogenic fungi (Fomitiporia mediterranea: 60%–90% and P. chlamydospora: 5%–15%) and by a few bacterial taxa (Sphingomonas spp. and Mycobacterium spp.). The occurrence of a specific association of fungal and bacterial species in cordons from young grapevines expressing esca-foliar symptoms strongly suggests that that microbiota is involved in the onset of this complex disease.