Peach RNA viromes in six different peach cultivars

www.nature.com/scientificreports OPEN Peach RNA viromes in six different peach cultivars Yeonhwa Jo1, Sen Lian2, Hyosub Chu1, Jin Kyong Cho3, Su-Hyun Yoo1, Hoseong Choi1, Ju-Yeon Yoon4, Seung-Kook Choi4, Bong Choon Lee5 & Won Kyong Cho 1,3 Received: 23 May 2017 Accepted: 16 January 2018 Published: xx xx xxxx Many recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars. The peach is a kind of popular stone fruits in the world. Peach [Prunus persica (L.) Batch] belongs the genus Prunus which includes almond, apricot, cherry, and plum1. In Korea, the peach is the third fruit tree, which is widely cultivated after apple and mandarin. Diverse peach cultivars with different harvest times are being cultivated due to their short storage times. Peach cultivars are clonally propagated to maintain fruit traits via grafting. Viruses and viroids infecting peach trees can be transmitted by grafting using virus-infected materials. To date, more than 20 different viruses infecting peach trees have been identified. Of known viruses infecting peach trees, Apple chlorotic leaf spot virus (ACLSV; genus Trichovirus), Plum pox virus (PPV; genus Potyvirus), Prunus necrotic ringspot virus (PNRSV; genus Ilarvirus), and Plum bark necrosis stem pitting-associated virus (PBNSPaV; genus Ampelovirus)2–5. Furthermore, the peach is susceptible to two different viroids including Hop stunt viroid (HSVd; genus Hostuviroid) and Peach latent mosaic viroid (PLMVd; genus Pelamoviroid)6,7. Although most peach trees infected by HSVd and PLMVd are asymptomatic, some PLMVd isolates cause severe disease symptoms such as albinism, leaf mosaics and blotches8. Thus far, the identification of the viruses and viroids that infect plants relies on collecting samples displaying viral disease symptoms followed by direct detection using RT-PCR and ELISA9,10. However, such approaches have only led to the identification of known viruses and viroids, rather than novel viral pathogens. Several next-generation sequencing (NGS)-based approaches have been conducted to overcome traditional approaches, which has resulted in the identification of known and novel viruses11–13. For example, two recent studies using NGS identified novel viruses in nectarines that might be responsible for stem-pitting disease symptoms14,15. Moreover, a recent study using NGS reported a novel virus referred as Peach leaf pitting-associated virus (PLPaV) in the genus Fabavirus, which is responsible for a leaf symptom16. Furthermore, peach-assoicated luteovirus and Peach virus D (PeVD) are also newly identified using NGS17,18. The term “virome” is defined as the genomes of all the viruses inhabiting a specific organism or environment19. In fact, many horticultural plants that are usually clonally propagated are reservoirs of a large variety of viruses and viroids. However, although studies associated with a single virus infection in a specific plant are numerous, 1 Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. 2College of Crop Protection and Agronomy, Qingdao Agricultural University, Qingdao, Shandong, 266109, China. 3The Taejin Genome Institute, Hoeongseong, Gadam-gil 61, 25239, Republic of Korea. 4Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, 565-852, Republic of Korea. 5Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea. Correspondence and requests for materials should be addressed to W.K.C. (email: ) SCIeNtIfIC REPOrtS | (2018) 8:1844 | DOI:10.1038/s41598-018-20256-w 1 www.nature.com/scientificreports/ Figure 1. The diverse phenotypes of the different peach cultivars and the experimental scheme. (a) A mature peach tree of the JT cultivar showing vigorous growth, (b) Healthy peach leaves without viral disease symptoms, (c) A peach branch with a young peach fruit and peach leaves showing viral disease symptoms, (d) A mature peach fruit without viral disease symptoms, (e and f) Peach leaves with viral disease symptoms. Peach fruits obtained from six examined peach trees. In general, the peach fruits were wrapped in a yellow envelope for the production of high quality fruit, (h) Experimental scheme of a peach virome study composed of wet experiment and dry experiment. viromes or viral populations in a particular plant have not been intensively examined. Thus far, only a limited number of studies have revealed viromes in specific plants such as grapevines20–22, sweet potato23, and pepper24. Furthermore, NGS-based approaches enable the assembly of viral genomes and reveal single nucleotide variations of present viruses24–26. Although peach is an important fruit tree; however, the studies associated with viruses and viroids infecting peach trees in Kore are limited. In this study, we conducted a peach RNA virome study in six different peach cultivars, which are commercially important in Korea. We identified both known viruses and viroids and a novel virus. In addition, the peach RNA virome reveals host specific viral communities in different peach cultivars, but unique viral communities of each peach plant associated with variety of factors. Results Preparation of samples, library construction, and RNA-Seq for metatranscriptome analyses. We initially examined an infection of Apple chlorotic leaf spot virus (ACLSV; genus Trichovirus) and two viroids (HSVd and PLMVd) in various peach trees by RT-PCR to study the peach virome in different peach cultivars. The RT-PCR results demonstrated that most peach trees were infected by at minimum either ACLSV or PLMVd. Most peach trees used in this study grew vigorously (Fig. 1a) and did not display any severe (...truncated)