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.
Highlights
The history of grapevines and viticulture is intertwined with that of early human civilisations
In this study we assessed the evolutionary history of grapevine leafroll-associated virus 3 (GLRaV-3), the type strain of the genus Ampelovirus, and determined the phylogenetic placement of a new genetic variant, isolate GH24 (KM058745)
Most previous studies of GLRaV-3 have concentrated on the RNA-dependent RNA polymerase (RdRp), the coat protein (CP) and the heat shock protein 70 homologue gene (Hsp70h) [5,36,37,38,39,40,41,42], which for most known isolates, are the only sequence data currently available
Summary
The history of grapevines and viticulture is intertwined with that of early human civilisations. Grapevine is susceptible to intracellular pathogens, of which many cause disorders that reduce plant vigour and longevity, as well as yield and quality of the harvest [4]. Infectious intracellular agents such as viruses, viroids, and phloem- or xylem-limited prokaryotes, of which there are more than 70 known species, are some of the most important pathogens affecting grapevine [4]. The most economically important viral disease is Grapevine Leafroll Disease (GLD) with grapevine leafroll-associated virus 3 (GLRaV-3) being the most prevalent associated virus [5]. The origin of GLD remains vague, but it may have been in the “Old World”, predating the widespread use of phylloxera-resistant rootstocks from the USA [5]
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