Peach RNA viromes in six different peach cultivars

Jo, Yeonhwa; Lian, Sen; Chu, Hyosub; Cho, Jin Kyong; Yoo, Su-Hyun; Choi, Hoseong; Yoon, Ju-Yeon; Choi, Seung‐Kook; Lee, Bong Choon; Cho, Won Kyong

doi:10.1038/s41598-018-20256-w

Cited by 62 publications

(74 citation statements)

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“…A virome study should include viral genome information for not only a single virus but also multiple viruses. Moreover, a virome study reveals not only the presence of viruses but also the complexity of viral genomes, viral replication, viral mutation, and the change of viral genomes in a certain condition, as shown previously 24,26,27 . Research associated with viruses infecting sweet potato has been intensively conducted in many countries 14,17,23,30 .…”

Section: Discussionsupporting

confidence: 68%

“…Although studies associated with viruses infecting sweet potato have been intensively conducted, there has not yet been a comprehensive study using NGS techniques for sweet potato viromes. As shown previously in our studies, RNA-Seq is a very powerful tool to study viromes in diverse plants [24][25][26][27] . Here, we conducted a study of sweet potato viromes by RNA-Seq.…”

supporting

confidence: 70%

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Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Kim

Choi

et al. 2020

Sci Rep

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The sweet potato in the family Convolvulaceae is a dicotyledonous perennial plant. Here, we conducted a comprehensive sweet potato virome study using 10 different libraries from eight regions in Korea and two different sweet potato cultivars by RNA-Sequencing. Comprehensive bioinformatics analyses revealed 10 different virus species infecting sweet potato. Moreover, we identified two novel viruses infecting sweet potato referred to as Sweet potato virus E (SPVE) in the genus Potyvirus and Sweet potato virus F (SPVF) in the genus Carlavirus. Of the identified viruses, Sweet potato feathery mottle virus (SPFMV) was the dominant virus followed by Sweet potato virus C (SPVC) and SPVE in Korea. We obtained a total of 30 viral genomes for eight viruses. Our phylogenetic analyses showed many potyvirus isolates are highly correlated with geographical regions. However, two isolates of SPFMV and a single isolate of Sweet potato virus G (SPVG) were genetically distant from other known isolates. The mutation rate was the highest in SPFMV followed by SPVC and SPVG. Two different sweet potato cultivars, Beni Haruka and Hogammi, were infected by seven and five viruses, respectively. Taken together, we provide a complete list of viruses infecting sweet potato in Korea and diagnostic methods. The sweet potato [Ipomoea batatas (L.) Lam] is a dicotyledonous perennial plant and a member of the family Convolvulaceae. It is currently widely grown in tropical and temperate regions in the world 1. The sweet potato is regarded as one of the most healthful foods in the world due to its high amounts of beta-carotene, carbohydrates, and dietary fiber and diverse micronutrients 2,3. It is a very fast-growing vine plant and is usually vegetatively propagated by cutting a piece of a runner of sweet potato approximately 30 cm in length 4. According to the FAO, in 2017, China was the largest sweet potato producer (72,031,782 tons), followed by several African countries, such as Malawi (5,472,013 tons), the United Republic of Tanzania (4,244,370 tons), and Nigeria (4,013,786 tons). In Korea, the sweet potato has been cultivated since the end of the 18th century, and it is the third most important crop plant in South Korea based on production (331,514 tons) 5. In general, the tuberous roots and stems of the sweet potato are used as different food materials in Korea. Due to their vegetative propagation, most sweet potato cultivars are severely infected by various pathogens. Of the known pathogens, more than 30 different viruses infecting sweet potato have been identified so far 6. The most frequently identified viruses are DNA viruses such as Sweet potato leaf curl virus (SPLCV) in the genus Begomovirus in the family Geminiviridae, followed by RNA viruses in the family Potyviridae 7. Examples of well-known RNA viruses infecting sweet potato include Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), Sweet potato latent virus (SPLV), and Sweet potato mild mottle virus (SP...

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Section: Discussionsupporting

confidence: 68%

supporting

confidence: 70%

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Kim

Choi

et al. 2020

Sci Rep

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“…Regarding fruit trees, in the last five years HTS use has led to the discovery of many new viruses [7–12]. Similarly to the present work, RNA viromes are detected in six peach trees identifying up to six viruses and viroids in each tree [13]. HTS data in nectarine provided insight to the etiology of stem pitting disease [14].…”

Section: Introductionsupporting

confidence: 55%

Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses

Rumbou

Candresse

Marais

et al. 2019

Preprint

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25 High-throughput sequencing (HTS), combined with bioinformatics for de novo discovery and 26 assembly of plant virus or viroid genome reads, has promoted the discovery of abundant novel 27 DNA and RNA viruses and viroids. However, the elucidation of a viral population in a single plant is 28 rarely reported. In five birch trees of German and Finnish origin exhibiting symptoms of birch leaf-29 roll disease (BRLD), we identified in total five viruses, among which three are novel. The number of 30 identified virus variants in each transcriptome ranged from one to five. The novel species are 31 genetically -fully or partially -characterized, they belong to the genera Carlavirus, Idaeovirus and 32 Capillovirus and they are tentatively named birch carlavirus, birch idaeovirus, and birch 33 capillovirus, respectively. The only virus systematically detected by HTS in symptomatic trees 34 affected by the BRLD was the recently discovered birch leafroll-associated virus. The role of the 35 new carlavirus in BLRD etiology seems at best weak, as it was detected only in one of three 36 symptomatic trees. Continuing studies have to clarify the impact of the carlavirus to the BLRD. The 37 role of the Capillovirus and the Idaeovirus within the BLRD complex and whether they influence 38 plant vitality need to be investigated. Our study reveals the viral population in single birch trees and 39 provides a comprehensive overview for the diversities of the viral communities they harbor. 40 41 Keywords: Betula sp., virome, birch leaf-roll disease, birch carlavirus, birch idaeovirus, birch 42 capillovirus 3 44 Introduction 45 Symptoms in birch trees (Betula sp.) caused by various viruses and related to the birch 46 leaf-roll disease (BLRD) are observed throughout Europe [1-2]. Diseased birches exhibit foliar 47 disorders including vein banding, leaf roll, mottling, necrotic lesions and tip dieback. Based on 48 earlier studies on virus-diseased trees it is assumed that BLRD might significantly reduce the tree's 49 photosynthetic capacity and contribute to tree decline [3]. Due to lack of knowledge, risk analyses 50 and prevention measures, the disease has effectively spread throughout Europe and has until now 51 been reported in European countries with diverse climatic conditions such as Finland, Sweden, 52 Norway, Germany, Austria, UK and France, including stands of a Mediterranean island [2-5]. 53The initial hypothesis for the BLRD disease etiology implicated Cherry leaf roll virus (CLRV) 54 as the disease main causal agent [1-2; 4-5]. However, after long-lasting trials applying 55 conventional viral detection methods (virus purification, RT-PCR, double-stranded-RNA isolation, 56 virus mechanical transmission), this virus could not be convincingly associated with the 57 appearance of disease symptoms. To identify BLRD etiology, a birch metagenomic study was 58 therefore initiated. A RNA-Seq analysis revealed for the first time in diseased trees from Germany 59 and Finland birch leafroll-associated virus (BLRaV), the first reverse-tra...

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“…To identify differences in the phytobiome between compartments and genotypes, we ran ParaKraken on endosphere, rhizosphere, and soil samples from P. deltoides and P. deltoides x P. trichocarpa (a hybrid). To mirror commonly used mapping methods in recent publications aimed at characterizing plant viriomes [21][22], the samples were initially analyzed using only the NCBI databases of all publicly available genomes from prokaryotes, archaes, eukaryotes and 8,000 viral taxa. The NCBI databases resulted in 50% of the 4.8 billion reads being assigned to taxa, with the rest representing unknown microbial dark matter ( Fig.…”

Section: Populus Metagenomementioning

confidence: 99%

A K-mer Based Approach for Virus Classification Identifies Coronavirus Infections and Viral Associations in Human and Plant Microbiomes

Garcia¹,

Simha²,

Garvin³

et al. 2020

Preprint

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BackgroundViruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples.MethodsTo identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken (a parallelized version of Kraken), a metagenomic/transcriptomic classifier. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2.ResultsTo illustrate the breadth of our utility for classifying viruses with ParaKraken, especially samples without virus-induced pathophysiology, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain tissue. In the Populus study, we identified genotype and compartment-specific viral signatures, while in the Autism study we identified a significant increase in abundance of eight viral sequences in post mortem brains. We also show the potential accuracy for classifying viruses by utilizing the NCBI viral databases to identify the uniqueness of viral sequences and to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples.ConclusionViruses represent an essential component of the microbiome. The ability to classify viruses represents the compulsory first step in better understanding their role in the microbiome. The viral classification method presented here allows for a more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members and can be used with any tool that utilizes a taxonomy for classification (such as Kraken).

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Peach RNA viromes in six different peach cultivars

Cited by 62 publications

References 54 publications

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses

A K-mer Based Approach for Virus Classification Identifies Coronavirus Infections and Viral Associations in Human and Plant Microbiomes

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