Genetic Dissection of Plasmopara viticola Population from a Greek Vineyard in Two Consecutive Years

Oilspots of the Plasmopara viticola population in a Greek vineyard over 2 years were collected and the pathogen genotyped with the use of four microsatellite loci. In 2001, five samplings occurred and 327 lesions were collected, which were classified to 23 genotypes. In 2002, the 426 lesions collected in four samplings belonged to 54 genotypes. A reproducible pattern of the evolution of the epidemic was exhibited that can be described as 'predominance-of-one-clone'. In 2001, the predominant clone covered 72-92% of each sample, while in 2002 the incidence of the predominant clone was 38-90%. The remaining genotypes showed low clonal reproduction and dispersal. Oosporic infections occurred throughout the season. The severity and the diversity in 2002 were, however, higher than in 2001 and this was not in accordance with the climatic conditions, suggesting that other factors, like the epidemic of the previous year, also influence the epidemic of the disease. These results produce new concepts about the epidemiology of the pathoge

Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.Peer Reviewe

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.Peer reviewe

Genetic Dissection of Plasmopara viticola Population from a Greek Vineyard in Two Consecutive Years

Oilspots of the Plasmopara viticola population in a Greek vineyard over 2 years were collected and the pathogen genotyped with the use of four microsatellite loci. In 2001, five samplings occurred and 327 lesions were collected, which were classified to 23 genotypes. In 2002, the 426 lesions collected in four samplings belonged to 54 genotypes. A reproducible pattern of the evolution of the epidemic was exhibited that can be described as 'predominance-of-one-clone'. In 2001, the predominant clone covered 72–92% of each sample, while in 2002 the incidence of the predominant clone was 38–90%. The remaining genotypes showed low clonal reproduction and dispersal. Oosporic infections occurred throughout the season. The severity and the diversity in 2002 were, however, higher than in 2001 and this was not in accordance with the climatic conditions, suggesting that other factors, like the epidemic of the previous year, also influence the epidemic of the disease. These results produce new concepts about the epidemiology of the pathogen.ISSN:0929-1873ISSN:1573-846

Population genetic structure of Plasmopara viticola after 125 years of colonization in European vineyards

To examine the within- and among-population genetic structure of Plamopara viticola oosporic populations in Europe, 8991 lesions from 32 vineyard plots were collected and analysed. Four multi-allelic microsatellite markers were used to genotype the pathogen. All populations had high levels of gene and genotypic diversity. Most populations were in Hardy-Weinberg equilibrium and thus randomly mating. Among P. viticola populations, significant low to moderate genetic differentiation was observed, even between geographically close populations. This genetic differentiation was also evident in the neighbour-joining phylogenetic genetic distance tree, showing clear substructure and distinguishing mainly five clusters based on geographical origin. Significant isolation by distance was found in central European P. viticola populations, suggesting a step-wise migration model. No significant isolation by distance was found within Greek populations, most probably owing to natural geographical barriers such as the sea and mountains, as well as the frequent population bottlenecks occurring in these populations, preventing natural migration among populations. The high variability of P. viticola provides explanation for its successful infestation of the heterogeneous European vineyards in the last 125 years after its introduction

Identification of the Coding-Complete Genome Sequence of a Novel Cytorhabdovirus in Tilia cordata Showing Extensive Leaf Chloroses

The article processing charge was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 491192747 and the Open Access Publication Fund of Humboldt-Universität zu Berlin.Here, we report the coding-complete sequence (14,152 nucleotides [nt]) of a novel cytorhabdovirus detected in Tilia cordata and tentatively named cytorhabdovirus tiliae. The assumed genome organization is 3′-N-P-P3-M-G-p6-p6’-L-5′. The N gene encodes the putative nucleoprotein (59.1 kDa), P encodes the phosphoprotein (34.7 kDa), P3 encodes the movement protein (23.1 kDa), M encodes the matrix protein (23.1 kDa), G encodes a glycoprotein (64.4 kDa), and L encodes the viral RNA polymerase (247 kDa). P6 and P6’ are overlapping open reading frames (ORFs), which may encode gene products of 7.9 and 9.5 kDa, respectively, of unknown functions.Peer Reviewe

Emergence of "birch-leafroll disease" in Fennoscandia correlated with significant changes in Cherry leaf roll virus population

201

A novel <em>badnavirus</em> discovered from <em>Betula sp.</em> affected by birch leaf-roll disease.

In declining birches (Betula sp.) from different European stands affected by the "birch leaf-roll disease" (BLRD) a novel virus is identified by means of RNA-Seq virome analysis. The virus represents a new member in the genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated virus (BLRaV) and it is the first badnavirus found to infect birch. Complete genome sequences (7,862-7,864 nucleotides) of three viral isolates of Finnish and German origin have been determined. The virus sequences show a typical badnavirus organization with three major open reading frames (ORFs) and a fourth potential ORF overlapping with the end of ORF3. ORFs 1-2-3 show low level of amino acid identity to the corresponding proteins encoded by other badnaviruses, reaching a maximum of 44% identity (ORF3). Grapevine vein-clearing virus appears as the closest badnavirus when considering the polymerase region. So far, we can exclude evidence for presence of endogenous BLRaV elements in the birch genome, while evidence for the episomal activity of BLRaV is provided. The viral population holds significant haplotype diversity, while co-infection by different BLRaV variants are observed in single hosts. BLRaV presence is associated with the BLRD in both silver (B. pendula) and downy birch (B. pubescens). These results challenge the earlier hypothesis of a causal role of Cherry leaf roll virus in BLRD. Further work is now needed to finally prove that BLRaV is the causal agent for the BLRD

High genetic diversity at the inter-/intra-host level of Cherry leaf roll virus population associated with the birch leaf-roll disease in Fennoscandia

201