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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement and Virus Management of Small Fruit Crops

Location: Horticultural Crops Research

Title: Molecular characterization and population structure of a new ampelovirus associated with blackberry yellow vein disease

item Thekke-veetil, T
item Sabanadzovic, N
item Keller, Karen
item Martin, Robert - Bob
item Sabanadzovic, S
item Tzanetakis, I

Submitted to: Virus Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2013
Publication Date: 12/14/2013
Citation: Thekke-Veetil, T., Sabanadzovic, N.A., Keller, K.E., Martin, R.R., Sabanadzovic, S., Tzanetakis, I.E. 2013. Molecular characterization and population structure of a new ampelovirus associated with blackberry yellow vein disease. Virus Research. 178:234-240.

Interpretive Summary: Blackberry yellow vein disease (BYVD) has become recognized as the most important disease of this crop in the southeastern U.S. since it was first characterized in the early 2000s. Diagnostic tests developed originally were found to give negative results on more than 50% of symptomatic plants. Thus, an effort was undertaken to characterize other viruses that may be associated with this disease. It is now known that the disease is caused by a virus complex, and that the complex can involve different virus combinations that produce the same symptoms. In this effort we characterized a new Ampelovirus, that is similar to Grapevine leafroll-associated virus-3 (GLRaV-3) and other members of subgroup I in this genus. The virus is provisionally named Blackberry vein banding associated virus (BVBaV). Three genes of 25 isolates of BYVaV were sequenced to examine virus diversity and to be able to develop a reliable RT-PCR based detection assay. This study shows significant diversity among the virus isolates, but without any pattern based on geographic origin. The role of this virus in BYVD is under further investigation.

Technical Abstract: Blackberry yellow vein disease is the most important viral disease of blackberry in the United States. Experiments were conducted to characterize a new virus identified in symptomatic plants. Molecular analysis revealed a genome organization resembling Grapevine leafroll-associated virus 3, the type species of the genus Ampelovirus in the family Closteroviridae. The genome of the virus, provisionally named Blackberry vein banding associated virus (BVBaV), consists of 18,643 nucleotides and contains 10 open reading frames (ORFs). These ORFs encode closterovirid signature replication-associated and quintuple gene block proteins, as well as additional four proteins of unknown function. Phylogenetic analyses of taxonomically-relevant products consistently placed BVBaV in the same cluster with GLRaV-3 and other members of the subgroup I of the genus Ampelovirus. The population structure of the virus in the U.S. was studied using the replication associated polyprotein 1a, heat shock 70 homolog and minor coat proteins of 25 isolates. This study revealed significant intra-species variation without any clustering among isolates based on their geographic origin. Further analyses indicated that these proteins are under stringent purifying selections. High genetic variability and incongruent clustering of isolates suggested the possible involvement of recombination in the evolution of BVBaV.

Last Modified: 07/25/2017
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