Abstract
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.
Highlights
Viruses cause significant yield and quality losses in a wide variety of cultivated crops
In two weed samples, we identified the viruses that had not previously been found in Poland: clover yellow mosaic virus (ClYMV) (Potexvirus genus, Alphaflexiviridae family) on V. officinalis plants, and melandrium yellow fleck virus (MYFV) (Bromovirus genus, Bromoviridae family) on S. latifolia plants
Despite potentially high sensitivity and specificity, require specific prior knowledge of the target pathogens, and are not suitable for detection of unknown or unexpected pathogens. Their high specificity might limit the detection of different isolates, variants or strains of particular pathogens, which can lead to false negative results [32,33]
Summary
Viruses cause significant yield and quality losses in a wide variety of cultivated crops. Increasing international travel and the trade of plant material, as well as climate changes, enhance the risk of spreading and introducing new viruses and their vectors into production systems [1,2]. The interactions between viruses coinfecting the same host might affect their host range, transmission rate, virus accumulation and, as a consequence, the presence and intensity of symptoms [6,7,8,9]. Plant viruses can emerge in crops from reservoir wild plant hosts in which they are often asymptomatic. Spread from the reservoirs into a new environment with the establishment of productive infections and effective between-host transmission mechanism are steps that require emergence to occur [10]. Many wild plants appear to have multiple infections, including both acute and persistent viruses [11]. Novel viruses are being discovered rapidly in Plants 2020, 9, 820; doi:10.3390/plants9070820 www.mdpi.com/journal/plants
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