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

Jo, Yeonhwa; Choi, Hoseong; Lian, Sen; Cho, Jin Kyong; Chu, Hyosub; Cho, Won Kyong

doi:10.7717/peerj.9588

Cited by 9 publications

(9 citation statements)

References 49 publications

(71 reference statements)

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“…Similarly, in single peach trees multi-viral infection of up to six viruses and viroids was detected ( Jo et al, 2018 ). A multiplicity of viral infections was also shown in metagenome samples from single plum trees ( Jo et al, 2020 ). A possible explanation for the single viral infection in the maple tree could be the age of the tree; it was very young (approx.…”

Section: Discussionmentioning

confidence: 91%

Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest

et al. 2021

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While the focus of plant virology has been mainly on horticultural and field crops as well as fruit trees, little information is available on viruses that infect forest trees. Utilization of next-generation sequencing (NGS) methodologies has revealed a significant number of viruses in forest trees and urban parks. In the present study, the full-length genome of a novel Emaravirus has been identified and characterized from sycamore maple (Acer pseudoplatanus) – a tree species of significant importance in urban and forest areas – showing leaf mottle symptoms. RNA-Seq was performed on the Illumina HiSeq2500 system using RNA preparations from a symptomatic and a symptomless maple tree. The sequence assembly and analysis revealed the presence of six genomic RNA segments in the symptomatic sample (RNA1: 7,074 nt-long encoding the viral replicase; RNA2: 2,289 nt-long encoding the glycoprotein precursor; RNA3: 1,525 nt-long encoding the nucleocapsid protein; RNA4: 1,533 nt-long encoding the putative movement protein; RNA5: 1,825 nt-long encoding a hypothetical protein P5; RNA6: 1,179 nt-long encoding a hypothetical protein P6). Two independent NGS sequencing runs from the same symptomatic maple tree detected the same genome segments. For one of these sequencing runs the cDNA library was prepared using a primer targeting the conserved genome terminal region, known to be shared between emaraviruses genome segments. We suggest, therefore, that the six identified genome segments represent the complete genome of a novel emaravirus from maple, which we tentatively name maple mottle-associated virus (MaMaV). Phylogenetic and sequence homology analyses place this virus on the distinct “subgroup a” clade within the Emaravirus genus along with – among others – rose rosette virus, Actinidia emaravirus 2, and fig mosaic virus. Validation RT-PCR assays performed on symptomatic and non-symptomatic trees suggest that MaMaV may be the symptom-inducing virus in the diseased trees. To our knowledge, this is the first time an Emaravirus is described from maple and is fully genetically characterized. With the discovery of MaMaV, the genus Emaravirus comprising negative-sense single-stranded viruses with very divergent genomes – that were until recently overlooked – has substantially increased counting 22 established and putative members.

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Section: Discussionmentioning

confidence: 91%

Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest

et al. 2021

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“…However, BLAST results for such short sequences sometimes lead to misidentification, even though partial sequences are derived from a single viral sequence (Jo et al, 2017). Although several studies have identified novel viruses of stone fruits using NGS (Jo et al, 2018a(Jo et al, , 2020, no novel viruses or viroids of pear was identified in the present study. Nevertheless, the obtained information is useful for documenting the virosphere diversity of pear trees.…”

Section: Discussionmentioning

confidence: 66%

“…Detection of viruses using classic methods, such as ELISA and RT-PCR, is often limited in terms of identifying novel virus species ( Jeong et al, 2014 ; Ji et al, 2013 ). In addition to increasing the rate of virus discovery, NGS has been used to detect viruses and viroids in various fruit trees, including citrus, and peach ( Jo et al, 2018b , 2020 ; Xu et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…Advances in next-generation sequencing (NGS)-based approaches have furthered our understanding of viral genome variability and evolution as well as facilitated the identification of viral disease mechanisms, measurement of viral abundance and diversity, screening of asymptomatic viruses, detection of low viral titers in infected plants, and discovery of unknown viruses, thereby providing novel insights into the complexity of the viral biosphere. Several studies have previously used NGS to investigate viromesdefined as the collective genomes of viruses present in a specific host or environment-and documented the viromes of several crops (Akinyemi et al, 2016;Jo et al, 2017;Jo et al, 2018aJo et al, , 2020. Therefore, high-throughput sequencing (HTS) can be integrated into the diagnostics and management of viral diseases, even when previously unknown viruses are involved.…”

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confidence: 99%

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Identification of Plant Viruses Infecting Pear Using RNA Sequencing

Kim

Lee

Kim³

et al. 2021

Plant Pathol J

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Asian pear ( Pyrus pyrifolia ) is a widely cultivated and commercially important fruit crop, which is occasionally subject to severe economic losses due to latent viral infections. Thus, the aim of the present study was to examine and provide a comprehensive overview of virus populations infecting a major pear cultivar (‘Singo’) in Korea. From June 2017 to October 2019, leaf samples ( n = 110) of pear trees from 35 orchards in five major pear-producing regions were collected and subjected to RNA sequencing. Most virus-associated contigs matched the sequences of known viruses, including apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV). However, some contigs matched the sequences of apple green crinkle-associated virus and cucumber mosaic virus. In addition, three complete or nearly complete genomes were constructed based on transcriptome data and subjected to phylogenetic analyses. Based on the number of virus-associated reads, ASGV and ASPV were identified as the dominant viruses of ‘Singo.’ The present study describes the virome of a major pear cultivar in Korea, and looks into the diversity of viral communities in this cultivar. This study can provide valuable information on the complexity of genetic variability of viruses infecting pear trees.

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“…By contrast, DNA and RNA shotgun sequencing can reveal not only microbial communities but also all living organisms within the samples [25,26]. Viruses do not possess any conserved sequences like bacteria and fungi, therefore, RNA sequencing is frequently used to identify viruses infecting plants [27,28]. Although NGS followed by bioinformatic analyses can reveal the microbial community composition in detail, it might be difficult to distinguish viable microorganisms from NGS data.…”

Section: Introductionmentioning

confidence: 99%

Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits

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Kim

et al. 2021

IJMS

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Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.

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

Cited by 9 publications

References 49 publications

Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest

Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest

Identification of Plant Viruses Infecting Pear Using RNA Sequencing

Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits

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