Population structure of blackberry chlorotic ringspot virus in the United States

High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

High Throughput Sequencing For Plant Virus Detection and Discovery

Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.

Quarantine Regulations and the Impact of Modern Detection Methods

Producers worldwide need access to the best plant varieties and cultivars available to be competitive in global markets. This often means moving plants across international borders as soon as they are available. At the same time, quarantine agencies are tasked with minimizing the risk of introducing exotic pests and pathogens along with imported plant material, with the goal to protect domestic agriculture and native fauna and flora. These two drivers, the movement of more plant material and reduced risk of pathogen introduction, are at odds. Improvements in large-scale or next-generation sequencing (NGS) and bioinformatics for data analysis have resulted in improved speed and accuracy of pathogen detection that could facilitate plant trade with reduced risk of pathogen movement. There are concerns to be addressed before NGS can replace existing tools used for pathogen detection in plant quarantine and certification programs. Here, we discuss the advantages and possible pitfalls of this technology for meeting the needs of plant quarantine and certification.

Next-generation sequencing of elite berry germplasm and data analysis using a bioinformatics pipeline for virus detection and discovery

Berry crops (members of the genera Fragaria, Ribes, Rubus, Sambucus, and Vaccinium) are known hosts for more than 70 viruses and new ones are identified continually. In modern berry cultivars, viruses tend to be asymptomatic in single infections and symptoms only develop after plants accumulate multiple viruses. Most certification programs are based on visual observations. Infected, asymptomatic material may be propagated in the nursery system and shipped to farms where plants acquire additional viruses and develop symptoms. This practice may result in disease epidemics with great impact to producers and the natural ecosystem alike. In this chapter we present work that allows for the detection of known and discovery of new viruses in elite germplasm, having the potential to greatly reduce virus dispersal associated with movement of propagation material.

Population structure of blueberry mosaic associated virus: Evidence of reassortment in geographically distinct isolates

The population structure of blueberry mosaic associated virus (BlMaV), a putative member of the family Ophioviridae, was examined using 61 isolates collected from North America and Slovenia. The studied isolates displayed low diversity in the movement and nucleocapsid proteins and low ratios of non-synonymous to synonymous nucleotide substitutions, indicative of strong purifying selection. Phylogenetic analyses revealed grouping primarily based on geography with some isolates deviating from this rule. Phylogenetic incongruence in the two regions, coupled with detection of reassortment events, indicated the possible role of genetic exchange in the evolution of BlMaV.

Epidemiology of Blackberry chlorotic ringspot virus

The pollen- and seed-borne ilarviruses pose a substantial threat to many specialty crops, including berries, rose, and tree fruit, because there are no efficient control measures other than avoidance. The case of Blackberry chlorotic ringspot virus (BCRV) is of particular interest because the virus has been found to be an integral part of blackberry yellow vein disease and is widespread in rose plants affected by rose rosette disease. This study provides insight into the epidemiology of BCRV, including incidence in blackberry and rose; host range, with the addition of apple as a host of the virus; and seed transmission that exceeded 50% in rose. Sensitive detection protocols that can be used to avoid dissemination of infected material through nurseries and breeding programs were also developed.