A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing

PLOS ONE, Dec 2019

A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.

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A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing

Naidu RA (2013) A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing. PLoS ONE 8(6): e64194. doi:10.1371/journal.pone.0064194 A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next- Generation Sequencing Sudarsana Poojari 0 Olufemi J. Alabi 0 Viacheslav Y. Fofanov 0 Rayapati A. Naidu 0 Darren P. Martin, Institute of Infectious Disease and Molecular Medicine, South Africa 0 1 Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America , 2 Eureka Genomics, Sugar Land, Texas , United States of America A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleafassociated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Francassociated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms. - Funding: This work was supported, in part, by Washington State Universitys Agricultural Research Center in the College of Agricultural, Human, and Natural Resource Sciences, Wine Advisory Committee of the Washington Wine Commission, USDA-Northwest Center for Small Fruits Research, USDA-NIFA Specialty Crop Research Initiative (Award Number 2009-51181-06027), Washington State Department of Agriculture Nursery Assessment Funds, Washington State Commission on Pesticide Registration and USDA-APHIS National Clean Plant Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have the following interests to report: Viacheslav Y. Fofanov is employed by Eureka Genomics. There are no patents, products in development or marketed products to declare. This does not alter the authors adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors. Nearly seventy viruses and other infectious sub-cellular obligate parasites, collectively referred to as graft-transmissible agents (GTAs), have been documented in grapevines (Vitis spp.) [1], [2]. Among all diseases caused either directly or indirectly by these GTAs, grapevine leafroll disease is considered as the most economically important disease affecting plant vigor and longevity and causing significant losses in fruit yield and impacting berry quality attributes [3], [4], [5]. Other virus diseases, such as rugose wood complex, fanleaf infectious degeneration and fleck complex, represent a group of disorders distributed widely in several grapegrowing countries around the world [1], [2]. Besides these traditional virus diseases, which can cause significant problems to grape production, other diseases due to GTAs have limited geographic distribution causing relatively less economic damage to grape production. In addition to viruses, several viroids belonging to the family Pospiviroidae are ubiquitous in cultivated grapevines [6], [7], [8], [9]. They are Hop stunt viroid (HpSVd, genus Hostuviroid), Grapevine yellow speckle viroid 1 (GYSVd-1, genus Apscaviroid) and 2 (GYSVd-2, ge (...truncated)


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Sudarsana Poojari, Olufemi J. Alabi, Viacheslav Y. Fofanov, Rayapati A. Naidu. A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing, PLOS ONE, 2013, 6, DOI: 10.1371/journal.pone.0064194