Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

Wu, Qingfa; Ding, Shou‐Wei; Zhang, Yongjiang; Zhu, Shuifang

doi:10.1146/annurev-phyto-080614-120030

Cited by 180 publications

(142 citation statements)

References 119 publications

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“…Recent rapid advances of next-generation sequencing (NGS) facilitate the identification of novel plant viruses and assembly of viral genomes 20–22 . Several different kinds of libraries have been prepared by using small RNAs, double-stranded (ds) RNAs, mRNAs, and ribosomal RNA-depleted total RNAs for NGS.…”

Section: Introductionmentioning

confidence: 99%

Barley RNA viromes in six different geographical regions in Korea

Bae

Kim

et al. 2018

Sci Rep

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Barley is a kind of cereal grass belonging to the family Poaceae. To examine viruses infecting winter barley in Korea, we carried out a comprehensive study of barley RNA viromes using next-generation sequencing (NGS). A total of 110 barley leaf samples from 17 geographical locations were collected. NGS followed by extensive bioinformatics analyses revealed six different barley viromes: Barley yellow mosaic virus (BaYMV), Barley mild mosaic virus (BaMMV), Barley yellow dwarf virus (BYDV), Hordeum vulgare endornavirus (HvEV), and Barley virus G (BVG). BaYMV and HvEV were identified in all libraries, while other viruses were identified in some specific library. Based on the number of virus-associated reads, BaYMV was a dominant virus infecting winter barley in Korea causing yellow disease symptoms. We obtained nearly complete genomes of six BaYMV isolates and two BaMMV isolates. Phylogenetic analyses indicate that BaYMV and BaMMV were largely grouped based on geographical regions such as Asia and Europe. Single nucleotide polymorphisms analyses suggested that most BaYMV and BaMMV showed strong genetic variations; however, BaYMV isolate Jeonju and BaMMV isolate Gunsan exhibited a few and no SNPs, respectively, suggesting low level of genetic variation. Taken together, this is the first study of barley RNA viromes in Korea.

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Section: Introductionmentioning

confidence: 99%

Barley RNA viromes in six different geographical regions in Korea

Bae

Kim

et al. 2018

Sci Rep

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“…In relation to quarantine controls, the NGS technique also allows reducing costs aiming the introduction of a new genetic material in a country . For the implementation of this new technique, it is essential to have support from the field of bioinformatics allied to the executor laboratory, as it will be necessary to process and analyze a large number of nucleotide sequences (WU et al, 2015).…”

Section: Advances Observed In Phytosanitary Diagnostic Methodsmentioning

confidence: 99%

Advances in Propagation of Grapevine in the World

et al. 2017

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-Grapevine production by classical grafting methods and in commercial scale emerged over 130 years. This system remained handmade until the mid-1950s, when emerged the first international certification programs aimed at obtaining mother plants with high viral sanity. The necessity to increase the scale of production on industrial model and plant material production based on minimum morphological standards appeared at the end of the 1960s. Along the 1970s, research unlocked knowledge on semi-automated grafting, process hygiene, use of plant growth regulators and understanding of physiological events of rootstock-scion compatibility, callus formation and rooting. So, until the mid-2000s, certification schemes and propagation processes advanced little in technical standard. However, grapevine growing areas were expanded and demands for plant material increased, and new diseases emerged from contaminated nurseries. These new diseases (new viral complexes, phytoplasmas, bacteria and grapevine trunk diseases) were discovered by high-sensitivity diagnostic methods. Today, there is a new discussion on the nursery segment worldwide. The propagation techniques have been reviewed from the perspective of reducing the incidence of new diseases and minimum physiological damage of nursery plants during the production stages. Therefore, technological innovations regarding equipment, practices and production inputs have been incorporated in new certification schemes. However, despite these advantages, these schemes have become more complex and multidisciplinary than previous ones, bringing difficulties in adaptation of nurserymen. Index-terms: Vitis grafting, nursery, certification, grapevine cuttings. AVANÇOS OBSERVADOS NA PROPAGAÇÃO DE VIDEIRAS NO MUNDORESUMO -A propagação de videiras a partir dos métodos clássicos de enxertia e em escala comercial teve origem há mais de 130 anos. Este sistema permaneceu artesanal até meados da década de 1950, quando se iniciaram os primeiros programas internacionais de certificação com foco na obtenção de plantas básicas com elevada sanidade para vírus. No fim da década de 1960, surgiu a necessidade de aumentar a escala para produção em um modelo industrial em que a muda apresentasse um padrão morfológico mínimo. Ao longo da década de 1970, aprofundaram-se as pesquisas relacionadas à automatização da prática de enxertia, à higienização do processo, ao uso de reguladores de crescimento e ao entendimento dos eventos fisiológicos da compatibilidade entre enxerto e porta-enxerto, formação de calos e enraizamentos. Assim, até meados dos anos 2000, os esquemas de certificação e o processo de propagação pouco evoluíram em termos técnicos. Porém, a medida que a área vitícola foi expandindo e a demanda por mudas aumentando, verificou-se que novas doenças se alastravam em escala global a partir de viveiros contaminados. Estas novas doenças (complexos virais, fitoplasmas, bactérias e fungos causadores de podridões vasculares) foram sendo descobertas à medida que os métodos de diagnose avançaram...

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“…DsRNA extraction and purification has been suggested as an approach to increase viral sequences in sample preparation for NGS (Wu et al, 2015). In a metagenomics study of viruses in environmental samples, Roossinck (2012) used dsRNA-enriched samples and detected high levels of persistent viruses in plants.…”

Section: Revista Mexicana De Fitopatologíamentioning

confidence: 99%

“…Surveys of RNA viruses in plants and fungi have been conducted by extracting dsRNAs, analyzing Se ha sugerido la extracción y purificación de dsRNA como un método para aumentar las secuencias virales en la preparación de muestras de NGS (Wu et al, 2015). En un estudio metagenómico de virus en muestras ambientales, Roossinck (2012) utilizó muestras concentradas con dsRNA viral y detectó altos niveles de virus persistentes en plantas.…”

Section: Field Surveysunclassified

Extracción y purificación de dsRNAs largos de plantas infectadas con virus y hongos; aplicación en la detección e identificación de virus

Valverde

Torre-Almaráz²

2017

RMF

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Abstract. Various Resumen. Se utilizan varios métodos para realizar la extracción y purificación de ARN de doble cadena (dsRNA) largo de plantas y hongos. Los protocolos más utilizados consisten en la extracción de fenol y la unión selectiva de dsRNA a la celulosa. Los dsRNAs virales purificados de plantas y hongos se han analizado por electroforesis con gel y se han utilizado como herramienta complementaria para identificar virus. Asimismo, los dsRNAs se han utilizado como reactivos en PCR de transcriptasa reversa, clonación molecular, preparación de sondas y secuenciación de virus ARN. Se han descubierto muchos virus ARN y moléculas subvirales que infectan plantas y hongos utilizando protocolos de extracción de dsRNA. Las recientes mejoras a los métodos de extracción de dsRNA han aumentado la eficiencia y la rentabilidad. Se ha comprobado que el dsRNA viral se puede utilizar como reactivo inicial para la secuenciación de próxima generación de genomas virales.

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Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

Cited by 180 publications

References 119 publications

Barley RNA viromes in six different geographical regions in Korea

Barley RNA viromes in six different geographical regions in Korea

Advances in Propagation of Grapevine in the World

Extracción y purificación de dsRNAs largos de plantas infectadas con virus y hongos; aplicación en la detección e identificación de virus

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