Virology Division News: The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation

Adams, M. J.; Antoniw, J. F.; Bar‐Joseph, M.; Brunt, A.A.; Candresse, Thierry; Foster, Gary D.; Martelli, G. P.; Milne, R.G.; Fauquet, C. M.

doi:10.1007/s00705-004-0304-0

Cited by 396 publications

(55 citation statements)

References 10 publications

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“…When the amino acid sequences of the CPs were aligned, some new isolates were close to isolates identified previously, while others were notably distant. GarVA isolates SW3.1A (Mexico) and WA6 (Argentina) shared only 79% aa identity with one another, which places them slightly below the allexivirus species demarcation point of <80% aa identity between CPs of distinct allexivirus species [9], [10], [13], [14]. These two GarVA isolates shared only 82–86% sequence identity with other known isolates, whereas isolates SW3.1B (Mexico), WA7 (Argentina), and Bate1 (Australia) were more closely related to one another and with isolates described from Korea and Japan (94–99% aa identities).…”

Section: Resultsmentioning

confidence: 99%

The Global Trade in Fresh Produce and the Vagility of Plant Viruses: A Case Study in Garlic

Wylie

Saqib

et al. 2014

PLoS ONE

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As cuisine becomes globalized, large volumes of fresh produce are traded internationally. The potential exists for pathogens infecting fresh produce to hitchhike to new locations and perhaps to establish there. It is difficult to identify them using traditional methods if pathogens are novel, scarce, and/or unexpected. In an attempt to overcome this limitation, we used high-throughput sequencing technology as a means of detecting all RNA viruses infecting garlic (Allium sativum L.) bulbs imported into Australia from China, the USA, Mexico, Argentina and Spain, and those growing in Australia. Bulbs tested were grown over multiple vegetative generations and all were stably infected with one or more viruses, including two species not previously recorded in Australia. Present in various combinations from 10 garlic bulbs were 41 virus isolates representing potyviruses (Onion yellow dwarf virus, Leek yellow stripe virus), carlaviruses (Shallot latent virus, Garlic common latent virus) and allexiviruses (Garlic virus A, B, C, D, and X), for which 19 complete and 22 partial genome sequences were obtained, including the first complete genome sequences of two isolates of GarVD. The most genetically distinct isolates of GarVA and GarVX described so far were identified from Mexico and Argentina, and possible scenarios explaining this are presented. The complete genome sequence of an isolate of the potexvirus Asparagus virus 3 (AV3) was obtained in Australia from wild garlic (A. vineale L.), a naturalized weed. This is first time AV3 has been identified from wild garlic and the first time it has been identified beyond China and Japan. The need for routine generic diagnosis and appropriate legislation to address the risks to primary production and wild plant communities from pathogens spread through the international trade in fresh produce is discussed.

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Section: Resultsmentioning

confidence: 99%

The Global Trade in Fresh Produce and the Vagility of Plant Viruses: A Case Study in Garlic

Wylie

Saqib

et al. 2014

PLoS ONE

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“…x domestica ), has a wide range of infectious agents, which include fungi, bacteria, phytoplasma, viruses and viroids. One such virus, Apple stem grooving virus (ASGV), is the type member of the genus Capillovirus (family Flexiviridae ) [1]. It is a positive-sense RNA virus with a genome of approximately 6.5 kb, which is organised into two overlapping open reading frames (ORFs) [2].…”

Section: Introductionmentioning

confidence: 99%

High-throughput sequencing reveals small RNAs involved in ASGV infection

et al. 2014

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BackgroundPlant small RNAs (sRNAs) associated with virulent virus infections have been reported by previous studies, while the involvement of sRNAs in latent virus infection remains largely uncharacterised. Apple trees show a high degree of resistance and tolerance to viral infections. We analysed two sRNA deep sequencing datasets, prepared from different RNA size fractions, to identify sRNAs involved in Apple stem grooving virus (ASGV) infection.ResultssRNA analysis revealed virus-derived siRNAs (vsiRNAs) originating from two ASGV genetic variants. A vsiRNA profile for one of the ASGV variants was also generated showing an increase in siRNA production towards the 3′ end of the virus genome. Virus-derived sRNAs longer than those previously analysed were also observed in the sequencing data. Additionally, tRNA-derived sRNAs were identified and characterised. These sRNAs covered a broad size-range and originated from both ends of the mature tRNAs as well as from their central regions. Several tRNA-derived sRNAs showed differential regulation due to ASGV infection. No changes in microRNA, natural-antisense transcript siRNA, phased-siRNA and repeat-associated siRNA levels were observed.ConclusionsThis study is the first report on the apple sRNA-response to virus infection. The results revealed the vsiRNAs profile of an ASGV variant, as well as the alteration of the tRNA-derived sRNA profile in response to latent virus infection. It also highlights the importance of library preparation in the interpretation of high-throughput sequencing data.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-568) contains supplementary material, which is available to authorized users.

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“…Grapevine virus A and B (GVA and GVB), which belong to the Vitivirus genus, are also relevant [85]. GVA is related with the Kober stem grooving symptom, where severe grooving on the grafted stems occurs [86,87], while GVB is associated with the corky bark syndrome consisting of soft, rubbery and abnormal swelling of the basal internodes of the canes, longitudinal cracks and cork forming, typical of the rugose wood complex [88].…”

Section: Grape and Wine Biotechnology 14mentioning

confidence: 99%

Grapevine Biotechnology: Molecular Approaches Underlying Abiotic and Biotic Stress Responses

Armijo¹,

Espinoza²,

Loyola³

et al. 2016

Grape and Wine Biotechnology

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Grapevine is one of the most abundant crops worldwide, with varieties destined for fresh and dry consumption, as well as wine production. Unfortunately, grapevine plants are affected by both biotic and abiotic stresses, generating significant economic losses. These conditions can negatively impact grape cultivation at different stages: plant and berry development during pre-and post-harvest, production, fresh fruit processing and export, along with wine quality. Most of the grapevine varieties are susceptible to several pathogens and within this chapter, particular attention is given to fungi (Botrytis cinerea and Erysiphe necator) and viruses, since they are a worldwide concern. Within the latter, special focus is given to the grapevine leafroll disease, a complex and destructive infection. On the other hand, abiotic stress is also relevant in grapevine, and in this chapter it will be exemplified by UV-B radiation and its impact on growth and fruit development, plant adaptive responses and its relationship with the quality of grape berries for winemaking. The main biotic and abiotic grapevine stress factors are reviewed in this chapter, considering a special focus on biotechnological approaches carried out in order to address them and minimize their detrimental consequences.

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Virology Division News: The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation

Cited by 396 publications

References 10 publications

The Global Trade in Fresh Produce and the Vagility of Plant Viruses: A Case Study in Garlic

The Global Trade in Fresh Produce and the Vagility of Plant Viruses: A Case Study in Garlic

High-throughput sequencing reveals small RNAs involved in ASGV infection

Grapevine Biotechnology: Molecular Approaches Underlying Abiotic and Biotic Stress Responses

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