Artemis Rumbou

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

SUMMARY 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.

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.

Particular structure of Plasmopara viticola populations evolved under Greek island conditions

ABSTRACT Plasmopara viticola populations collected from three islands in the Ionian Sea-an arm of the Mediterranean Sea to the west of Greece-were analyzed with microsatellite molecular markers in order to investigate the pathogen population structure. Downy mildew populations from mainland regions previously studied were found to have high genotypic diversity and limited clonality; however, populations under Mediterranean island conditions mostly showed limited variation and the epidemics basically were driven by the multiple clonal infections of one or a few genotypes. Populations from different islands were differentiated from each other, whereas genetic divergence also was found among subpopulations of the same plot. Polyploid individuals and individuals that overwintered in asexual form were observed in some cases. The findings obtained by this population genetics study improve our understanding of the biology of the pathogen and lead to potential alternative control measures for the disease.

A model system for plant-virus interaction—infectivity and seed transmission of Cherry leaf roll virus (CLRV) in Arabidopsis thaliana

The wide natural incidence of Cherry leaf roll virus (CLRV) in deciduous forest trees and nurseries in northern Europe is believed to have occurred, apart from occasional mechanical spread and transmission through grafting, mainly by seed transmission. The mode of the vertical transmission and its role in the epidemiology of the virus has not been investigated, basically due to the inconvenient host-pathogen combinations studied to date. With the aim of obtaining an appropriate system for identification of viral genes and products participating in infection processes and seed transmission of CLRV, we performed infection and seed transmissibility tests with CLRV in Arabidopsis thaliana plants. Two phylogenetically and serologically different CLRV isolates were tested. Both of them were found able to infect A. thaliana plants, exhibited clear symptoms of the infection and spread systemically in the plants. Infection of the seeds and of a remarkable number of seedlings generated from infected seeds was possible for two consecutive generations. These results, for first time, report seed transmission of CLRV in the model plant A. thaliana and allow the assumption to be made of embryo invasion during seed transmission. Furthermore, first indications are given that genetically diverse CLRV isolates exhibit different abilities for vertical transmission in A. thaliana. The CLRV-A. thaliana model system is suitable for investigating viral invasion of developing plant organs and meristematic tissue, a prerequisite for successful virus dissemination via vertical transmission through seed.

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

ABSTRACT A viral epidemic associated with the Cherry leaf roll virus (CLRV) has emerged in Betula species in Fennoscandia, exhibiting quick and effective spread during the last 15 years. A population genetics approach is chosen in order to characterise the virus diversity and the sources of genetic variation aiming to investigate the epidemiology of the pathogen. In a CLRV population from Rovaniemi urban parks and a population that occurred after infecting young Betula seedlings with scions from the original Finnish trees, the genetic diversity is found to be remarkably high, mixed infections by CLRV variants from different phylogenetic groups are detected in single trees, while recombination is evidenced to occur. The estimated genetic variability is high and the CLRV haplotypes detected exhibit clear clustering and belong to different phylogenetic groups. The structure of the viral population reveals a pathogen with high evolutionary potential assumed to carry on its effective spread.

A novel badnavirus discovered from Betula sp. 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.