Fig 1.
Distribution of single and mixed infections in Vitis vinifera subsp. sylvestris (Gmeli) Hegi in Tuscany.
Detected infections with single and mixed infection (expressed as % of virus out of total number of analysed plants).
Fig 2.
Phylogenetic tree showing the distribution of Tuscan Grapevine rupestris stem pitting-associated virus (GRSPaV) coat protein nucleotide sequences.
Neighbour-joining tree shows the distribution of Tuscan GRSPaV coat protein nucleotide sequences compared to isolates from the GenBank. Geographical origin is given for each isolate (in brackets). Bootstrap values are from 1000 replicates.
Fig 3.
Phylogenetic tree showing the distribution of coat protein nucleotide sequences of Tuscan Grapevine leafroll-associated virus 1 (GLRaV-1).
The neighbour-joining tree shows the distribution of Tuscan GLRaV-1 coat protein nucleotide sequences compared to isolates from the GenBank. Geographical origin is given for each isolate (in brackets). Bootstrap values are from 1000 replicates.
Fig 4.
Recombination analysis by RDP4 of 29 coat protein nucleotide sequence alignments.
(A) MaxChi breakpoint matrix. MaxChi matrices are useful for identifying the statistically optimal positions of breakpoint pairs. Colors represent chi-squared values for different pairs of breakpoints; dark red peaks indicate the most probable positions of breakpoint pairs. (B) Tree display providing information on parental sequences (and phylogenetically plausible alternative parents). The red highlighted sequence is the currently selected recombinant sequence; green and blue indicate reasonably close relatives of major and minor parents; orange and pink have similar (Orange) or somewhat similar but notably different (Pink) recombination signals to that observed in the sequence highlighted in red.
Fig 5.
Phylogenetic tree showing the distribution of coat protein nucleotide sequences of Tuscan Grapevine virus A (GVA).
Neighbour-joining tree shows the distribution of Tuscan GVA coat protein nucleotide sequences compared to isolates from the GenBank. The geographical origin is provided for each isolate (in brackets). Bootstrap values are from 1000 replicates.
Fig 6.
Phylogenetic tree showing the distribution of coat protein nucleotide sequences of Tuscan Grapevine leafroll-associated virus 3 (GLRaV-3).
Neighbour-joining tree shows the distribution of Tuscan GLRaV-3 coat protein nucleotide sequences compared to isolates from the GenBank. Geographical origin is provided for each isolate (in brackets). Bootstrap values are from 1000 replicates.