Small RNA deep sequencing reveals the presence of multiple viral infections in cucurbit crops in Guangdong, China

Viral diseases are among the most critical damaging factors that impose a global threat to the cucurbit industry. China is the world's leading country for the production and consumption of cucurbits. Guangdong, a province in southern China dominated by the tropical and subtropical climate, favors the survival of different plant viruses and their vectors. Five main cucurbit crops showing various disease symptoms were surveyed and collected to identify viruses infecting cucurbits in Guangdong during 2018–2020. In the field, the incidence ranged from 5–30%, or even 60–100% in the case of severely infected cucurbits. A total of 357 symptomatic samples were collected and subsequently screened for cucurbit viruses by small RNA deep sequencing and assembly (sRSA). Seventeen virus species belonging to 10 genera were identified in the five main cucurbit crops. The most common viruses were papaya ringspot virus (PRSV; Potyvirus), zucchini tigre mosaic virus (ZTMV; Potyvirus), zucchini yellow mosaic virus (ZYMV; Potyvirus), and watermelon silver mottle virus (WSMoV; Orthotospovirus), with infection rates of 24.4, 19.0, 17.1, and 14.3%, respectively. Notably, the most prevalent viruses were melon yellow spot orthotospovirus (MYSV) in cucumber, PRSV in squash, cucumber green mottle mosaic virus (CGMMV; Tobamovirus) in bottle gourd, WSMoV in white gourd, and ZYMV in luffa. Mixed infections were prevalent, and the types of mixed infections varied substantially in different cucurbit crops. Moreover, the full-length nucleotide sequences of watermelon green mottle mosaic virus (WGMMV), CGMMV, and watermelon virus A (WVA; Wamavirus) identified in bottle gourd were cloned and analyzed. This study is the first reporting WGMMV infecting bottle gourd in China mainland. In summary, the results demonstrate that in Guangdong, the most prevalent viruses belong to potyviruses, orthotospoviruses, and tobamoviruses groups. The findings will facilitate agricultural researchers and farmers to plan and implement effective disease control strategies aiming at timely detection and management of cucurbit-infecting viral pathogens.