The virome of Lamon bean: application of MinION Sequencing to investigate the virus population associated with symptomatic beans in the Lamon area, Italy

Lamon bean is a protected geographical indication (PGI) for a product of four varieties of bean (Phaseolus vulgaris L.) grown in a specific area of production, which is located in Belluno district, Veneto region (N.E. of Italy). In the last decade, the Lamon bean has been threatened by severe virus epidemics that have compromised its profitability. The emergence of new viruses and novel viral strains has always represented the major cause of viral epidemics, leading to huge crop losses and threatening crop production. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing (Oxford Nanopore Technologies). Evidence that emerged from sequencing was validated through RT-PCR and ELISA in a large number of plants, including different ecotypes of Lamon bean and wild herbaceous hosts that may represent a virus reservoir in the field. Results revealed the presence of Bean common mosaic virus (BCMV), Cucumber mosaic virus (CMV), Peanut stunt virus (PSV), and Bean Yellow Mosaic Virus (BYMV), which often occurred as mixed infections. Moreover, both CMV and PSV were reported in association with strain-specific satellite RNAs (satRNAs). In conclusion, this work sheds light on the cause of the severe diseases affecting Lamon bean by exploitation of MinION sequencing.