title: Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus.
abstract: The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.
authors.affiliation: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Private Bag X5026, Stellenbosch, 7599, South Africa; Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Maree
authors.affiliation: Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-University, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany; Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Pirie
authors.affiliation: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Kristin
authors.initials: K
authors.lastname: Oosthuizen
authors.affiliation: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Rachelle
authors.initials: R
authors.lastname: Bester
authors.affiliation: Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa.
authors.forename: D Jasper G
authors.initials: DJ
authors.lastname: Rees
authors.affiliation: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Johan T
authors.initials: JT
authors.lastname: Burger
mesh_terms: D029381:Closteroviridae / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D011995:Recombination, Genetic; D027843:Vitis / Q000821:virology*