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Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing

Title
Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing
Authors
Jo, YeonhwaChoi, HoseongLian, SenCho, Jin KyongChu, HyosubCho, Won Kyong
Issue Date
2020-07
Citation
PeerJ, 8
Type
Article
Article Type
Article
Author Keywords
PlumRNA-seqViroidVirusKorea
Keywords
PITTING-ASSOCIATED-VIRUSSTONE FRUIT-TREES1ST REPORTPOX-VIRUSGENERATIONPEACHCHERRY
ISSN
2167-8359
Abstract
Background: Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees. Methods: To identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database. Results: We identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses - ACLSV, PBNSPaV, and PNRSV - in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea. © Copyright 2020 Jo et al.
URI
http://hdl.handle.net/20.500.11750/12394
DOI
10.7717/peerj.9588
Publisher
PeerJ Inc.
Files:
Collection:
ETC1. Journal Articles


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