The genetic variability of grapevine Pinot gris virus (GPGV) in Australia

Abstract

Grapevine Pinot gris virus (GPGV; genus Trichovirus in the family Betaflexiviridae) was detected in Australia in 2016, but its impact on the production of nursery material and fruit in Australia is still currently unknown. This study investigated the prevalence and genetic diversity of GPGV in Australia. GPGV was detected by reverse transcription-polymerase chain reaction (RT-PCR) in a range of rootstock, table and wine grape varieties from New South Wales, South Australia, and Victoria, with 473/2171 (21.8%) samples found to be infected. Genomes of 32 Australian GPGV isolates were sequenced and many of the isolates shared high nucleotide homology. Phylogenetic and haplotype analyses demonstrated that there were four distinct clades amongst the 32 Australian GPGV isolates and that there were likely to have been at least five separate introductions of the virus into Australia. Recombination and haplotype analysis indicate the emergence of new GPGV strains after introduction into Australia. When compared with 168 overseas GPGV isolates, the analyses suggest that the most likely origin of Australian GPGV isolates is from Europe. There was no correlation between specific GPGV genotypes and symptoms such as leaf mottling, leaf deformation, and shoot stunting, which were observed in some vineyards, and the virus was frequently found in symptomless grapevines.

Keywords: GPGV; Median joining network; Metagenomic HTS; Phylogenetic analysis; Population genetics; Recombination.

Fig. 1

The number of samples submitted to Crop Health Services Plant Diagnostic Laboratory from various grape growing regions in South Australia (SA), New South Wales (NSW) and Victoria (VIC) that tested positive or negative for grapevine Pinot gris virus (GPGV). The Sunraysia horticultural district encompasses growers located in northwest VIC and southwest NSW. Other NSW isolates in the image includes samples from various regions in that state. Image generated by tracing Google Maps (Scale = 20 km)

Fig. 2

Symptoms were observed in different table and wine grape varieties. Leaf mottling and deformation symptoms were observed in (a) Nero d’Avola; (b) Fiano; (c) Vermintino; (d) Malbec and zig-zag shoots observed in (e) Crimson seedless

Fig. 3

Maximum likelihood phylogenetic tree with 1000 bootstrap replicates of the 3′ end of movement protein and 5′ end of coat protein genes of the genome for 32 Australian grapevine Pinot gris virus (GPGV) isolates and 68 isolates from previous studies that were associated with grapevine leaf mottling and deformation disease (GLMD) or with asymptomatic infections in various grapevine varieties. Clade A (asymptomatic grapevines) and clades B and C (GLMD-affected grapevines) are based on the clades described previously [2, 6]. Bootstrap values (> 70%) are reported at the nodes

Fig. 4

Maximum likelihood tree inferred from thirty-two genome sequences of grapevine Pinot gris virus (GPGV) which were de novo assembled from high throughput sequencing (HTS) datasets (a) only Australian isolates; b full tree with 32 Australian and 168 overseas isolates published on GenBank; c collapsed tree to highlight the global relationships of Australian isolates to isolates from other regions. The number at each node indicates bootstrap percentages based on 1000 replicates. The scale bar corresponds to the number of substitutions per site. The percentage identity to each other for each clade is on the right

Fig. 5

Location of sample collection sites of GPGV isolates in different vine-growing regions of Australia. Image generated by tracing Google Maps (Scale = 20 km). Mildura refers to the Victorian area of the Sunraysia horticultural region surrounding the city of Mildura and which extends 60km from Yelta in the northwest and Colignan in the southeast

Fig. 6

Median-joining network showing grapevine Pinot gris virus (GPGV) variants dividing the isolates into four distinct clusters including 32 GPGV isolates from Australia and 19 overseas isolates. The sizes of the circles are proportional to the number of times each variant was observed. Unlabelled black dots (median vectors) are hypothetical intermediate variants connecting the variant groups. Numbers in the bracket infer the number of mutations separating the variants

Fig. 7

The location of the recombination events on the genome of four Australian grapevine Pinot gris virus (GPGV) isolates as detected by recombination-detection algorithms (RDP4 program)

Fig. 8

Hypothetical introductions of grapevine Pinot gris virus (GPGV) in Australia including the major and minor parents of predicted GPGV recombinants based on phylogenetic, median-joining (MJ) network and recombination analyses