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

doi:10.1016/S2095-3119(21)63661-4

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (5): 1389-1400.DOI: 10.1016/S2095-3119(21)63661-4

收稿日期:2021-01-14 接受日期:2021-02-19 出版日期:2022-05-01 发布日期:2021-02-19

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

LI Zheng-gang^1*, NONG Yuan^1*, Tahir FAROOQ¹, TANG Ya-fei¹, SHE Xiao-man¹, YU Lin¹, LAN Guo-bing¹, ZHOU Xue-ping^{2, 3}, HE Zi-fu¹

¹ Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R.China
² State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
³ State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R.China

Received:2021-01-14 Accepted:2021-02-19 Online:2022-05-01 Published:2021-02-19
About author:LI Zheng-gang, Tel: +86-20-87597476, E-mail: lzaagg@cau.edu.cn; NONG Yuan, Tel: +86-20-87597476, E-mail: 1650767942@qq.com; Correspondence HE Zi-fu, Tel: +86-20-87597476, E-mail: hezf@gdppri.com * These authors contributed equally to this study.
Supported by:
This work was supported by the grants from the National Natural Science Foundation of China (31801712), the Key Research and Development Program of Guangdong Province, China (2018B020202006), the Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences (202103TD and 202105TD), and the Development Program for Guangdong Province Modern Agricultural Science and Technology Innovation Alliance (2020KJ113).

摘要/Abstract

摘要：

本研究旨在明确侵染广东省瓜类作物病毒种类，为瓜类作物病毒病防控提供理论依据。2018-2020年，我们针对黄瓜、南瓜、葫芦、冬瓜、丝瓜等5种广东主要瓜类作物的病毒病进行了调查与监测，并采集了357个疑似病毒侵染的瓜类作物样品。将采集的样品提取总RNA后进行小RNA深度测序与组装分析，然后根据小RNA测序分析结果设计病毒特异引物进行RT-PCR验证，得出每个瓜类样品中的病毒种类，最后对结果进行统计分析。广东瓜类作物病毒病的田间病株率一般为5%-30%，在一些发病严重地块的病株率高达60%，甚至100%。在采集的5种瓜类作物样品中总共鉴定出归属于10个病毒属的17种病毒，其中检出率最高的病毒是番木瓜环斑病毒 (PRSV)、小西葫芦虎纹花叶病毒 (ZTMV)、小西葫芦黄花叶病毒 (ZYMV)、西瓜银斑驳病毒 (WSMoV)，检出率分别是24.4%、19.0%、17.1%、14.3%。5种瓜类作物样品中病毒种类不同，且优势病毒也明显不同，黄瓜上检出率最高的病毒是甜瓜黄化斑点病毒 (MYSV)，南瓜上是PRSV，葫芦上是黄瓜绿斑驳花叶病毒 (CGMMV)，冬瓜上是WSMoV，丝瓜上是ZYMV。一个样品中检测出多种病毒的复合侵染很普遍，不同的瓜类作物样品中复合侵染的形式也不一样。进一步分析发现CGMMV、西瓜绿斑驳花叶病毒 (WGMMV)、西瓜病毒A (WVA) 在葫芦上的复合侵染率很高。我们克隆了CGMMV、WGMMV、和WVA的基因组全长序列，遗传进化分析表明WGMMV与CGMMV的亲缘关系较近。本研究首次在中国大陆发现了WGMMV。广东最流行的瓜类作物病毒是马铃薯Y病毒属病毒 (potyvirus)、正番茄斑萎病毒属病毒 (orthotospovirus)、烟草花叶病毒属病毒 (tobamovirus)，其主要传播途径分别是蚜虫、蓟马及种子带毒。本研究为瓜类作物病毒病防控策略及防控措施的制订奠定了理论基础。

Abstract: 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.

Key words: cucurbit viruses , small RNA deep sequencing , phylogenic analyses , potyviruses , orthotospoviruses , tobamoviruses

. [J]. Journal of Integrative Agriculture, 2022, 21(5): 1389-1400.

LI Zheng-gang, NONG Yuan, Tahir FAROOQ, TANG Ya-fei, SHE Xiao-man, YU Lin, LAN Guo-bing, ZHOU Xue-ping, HE Zi-fu. Small RNA deep sequencing reveals the presence of multiple viral infections in cucurbit crops in Guangdong, China[J]. Journal of Integrative Agriculture, 2022, 21(5): 1389-1400.

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

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