The Virome of ‘Lamon Bean’: Application of MinION Sequencing to Investigate the Virus Population Associated with Symptomatic Beans in the Lamon Area, Italy

Abstract

‘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 the 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. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing. 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 the ‘Lamon bean’ by exploitation of MinION sequencing.

Surveillance of Landraces’ Seed Health in South Italy and New Evidence on Crop Diseases

“…Finally, BCMV was found in common bean and cowpea accessions [ 53 ]; in particular, on the former species, BCMV was sometimes associated with CMV. In Italy, mixed infection was documented in the Veneto region, starting from 2012 on the Lamon bean ( P. vulgaris ), an agricultural product obtained by the cultivation of four local varieties [ 54 ]. In addition, BCMV, as a single infective agent, was detected in 24% and 100% of the common bean and cowpea accessions tested, respectively.…”

Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses

“…In recent years, ONT has demonstrated success across a wide variety of plant viruses by generating long-read single-molecule sequence data in real time with an innovation in third-generation sequencing technology ( Jain et al, 2015 ; Lewandowski et al, 2019 ; Zhu et al, 2020 ). ONT has been used to detect plant viruses in a variety of plants, including peaches ( Bronzato Badial et al, 2018 ), tomatoes ( Chalupowicz et al, 2019 ), yams ( Filloux et al, 2018 ), potatoes ( Della Bartola et al, 2020 ), wheat ( Fellers et al, 2019 ), cowpea ( Naito et al, 2019 ), cassava ( Boykin et al, 2019 ), Medicago arborea ( Ben Chehida et al, 2021 ), Jasminum officinale ( Amoia et al, 2022 ), grapevine ( Javaran et al, 2021 ), roses ( Vazquez-Iglesias et al, 2022 ), and lamon bean ( Tarquini et al, 2022 ).…”