Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards

Abstract

Grapevine rupestris stem pitting-associated virus (GRSPaV; genus Foveavirus, family Flexiviridae) is present in many grape-growing regions of the world. A total of 84 full-length coat protein (CP) sequences and 57 sequences representing the helicase-encoding region (HR) of the RNA-dependent RNA polymerase were obtained from wine grape cultivars grown in the Pacific North-West (PNW) of the United States and their molecular diversity was compared with corresponding sequences previously reported from other grape-growing regions. In pairwise comparisons, the CP sequences from PNW isolates showed identities between 80 and 100 % at the nucleotide level and the HR sequences showed identities between 79 and 100 %. A global phylogenetic analysis of the CP and HR sequences revealed segregation of GRSPaV isolates into four major lineages with isolates from PNW distributed in all four lineages, indicating a lack of clustering by geographical origin. Scion cultivars grafted onto rootstock were found to contain mixtures of more genetic variants belonging to different lineages than own-rooted cultivars. Assessment of population genetic parameters found that the CP was more variable than the HR region. The discordant gene phylogenies obtained for some CP and HR sequences and the identification of potential recombination events involving parents from different lineages provided strong evolutionary evidence for genetic diversity among GRSPaV isolates. These results underscore the highly variable nature of the virus with implications for grapevine health status and distribution of virus-tested planting materials. This study also contributes to an increased understanding of molecular population genetics of viruses infecting deciduous woody perennials.

Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus

“…Similar results were described for coat protein genes of Grapevine rupestris stem pittingassociated virus (Alabi et al, 2010) and Sweet potato mild mottle virus (SPMMV) (Tugume et al, 2010). In contrast, animal viruses experience strong diversifying selection (Drummond et al, 2003;Yang and Bielawski, 2000) which is caused predominantly by pressure from the immune system of the host.…”

“…Comparison of amino acid sequences showed higher identities 78.2-99.5 %. Similar high levels of CP gene diversity are described for other members of the family Betaflexiviridae (Alabi et al, 2010;Teycheney et al, 2005). The lack of a biological vector for transmission of ASPV probably makes the CP more tolerant to sequence variability than the capsid proteins of vector borne plant viruses subjected to greater purifying selection on amino acid changes (Garcia-Arenal et al, 2001;Rubio et al, 2001;Vives et al, 2002).…”

Phylogenetic analysis and recombination events in full genome sequences of apple stem grooving virus

“…first time identified the two codons, at positions 1756 and 1798, under positive selection. Similar results were observed for the cp genes of apple stem pitting virus (Komorowska et al, 2011), grapevine rupestris stem pitting-associated virus (Alabi et al, 2010), sweet potato mild mottle virus (SPMMV) (Tugume et al, 2010), and the P1 proteinase of SPMMV (Tugume et al, 2010), where several codons were under positive selection whereas purifying selection acted on the other sites. Purifying selection could occur by functional constraints during the virus life cycle when interacting with hosts (Schneider and Roossinck, 2000;French and Stenger, 2003), and it is the main evolutionary force (García-Arenal et al, 2001).…”

Produção de antissoro policlonal utilizando a proteína capsidial recombinante do Rupestris stem pitting-associated virus

“…contando inclusive com a definição de quatro grupos de isolados por ALABI et al (2010), a produção de um antissoro contra a CP de um isolado específico desse vírus pode constituir-se em uma importante ferramenta para a detecção do RSPaV, se tal anticorpo apresentar a propriedade de reconhecer diferentes isolados.…”