DOI: 10.57745/fqfh8r
title: List of Supplemental methods and figures.docx

description: List of Supplemental methods:
Methods S1 Plasmopara viticola propagation.
Methods S2 Plasmopara viticola inoculation.
Methods S3 DNA extraction.
Methods S4 Sequencing.
Methods S5 Variant Calling.
Methods S6 Quality control.
Methods S7 Population structure.
Methods S8 Genome reassembly procedure and annotation.
Methods S9 Phylogenetic analyses of the avrRpv3.1-like gene sequences.
Methods S10 Population genetic analysis.
Methods S11 avrRpv3.1 locus analysis of the virulent strain avrRpv12-/3- and Pv412.
Methods S12 Gene expression analysis.
Methods S13 Infiltration experiment.

List of Supplemental Figures:
Fig. S1 Linear correlation between the sporulation area on Cabernet sauvignon and Regent.
Fig. S2 Histogram of the sporulation area of each of the 123 strains on Cabernet sauvignon and Regent.
Fig. S3 Principal component analysis realized with a subset of 18,069 SNPs.
Fig. S4 Quantile-quantile plot associated with Figure 1.
Fig. S5 Manhattan plot of scaffolds Plvit038 and Plvit053 where the significant loci are located.
Fig. S6 Alignment of the sequences of Plvit038 and Plvit053 against INRA-Pv221 reference genome.
Fig. S7 Alignment of the sequences of the Haplotig_000014F_004 against the Primary_000014F.
Fig. S8 Maximum likelihood phylogenetic tree of the 11 protein sequences of Plasmopara viticola identified as avrRpv3.1-like genes and three similar proteins found in the closely-related species Plasmopara hasltedii.
Fig. S9 Patterns of coverage in the locus (1/2).
Fig. S10 Patterns of coverage in the locus (2/2).
Fig. S11 Representation of the seven alleles identified in the 123 P. viticola strains analyzed in this study.
Fig. S12 Genomic structure at the avrRpv3.1 locus for each P. viticola strains associated with their phenotype.
Fig. S13 Patterns of coverage in the locus avrRpv3.1 of the strain "avrRpv12-/3-" from Wingerter et. al. (2021).
Fig. S14 Patterns of coverage in the locus avrRpv3.1 of the strain Pv412_11 from Paineau et. al. (2022).
Fig. S15 Distribution of Weir and Cockerham FST across the entire contig and the specific FST value computed for the avrRpv3.1 locus.
Fig. S16 Conserved amino-acid motifs in avrRpv3.1-like proteins.
Fig. S17 Predicted tertiary structure of (A) g164, (B) g165, (C) g166 and (D) the superimposition of the three of them. 
Fig. S18 Confidence metrics of the g164 predicted tertiary structure.
Fig. S19 g164 structural domains do not fit the LWY domain fold.
Fig. S20 PCRs on genomic DNA from P. viticola strain Pv221 and the strain 'Pv412_11'.
Fig. S21 Candidate effector genes from the AvrRpv3.1 locus are expressed in germinated spores and infected tissues.
Fig. S22 Candidate effector proteins from the AvrRpv3.1 locus induce cell death in plants carrying Rpv3. 
Fig. S23 Candidate effector proteins from the AvrRpv3.1 locus induce cell death in plants carrying Rpv3. 
Fig. S24 Candidate effector proteins from the AvrRpv3.1 locus induce cell death in plants carrying Rpv3.1. (6 days post-agroinfiltration) 
Fig. S25 Candidate effector proteins from the AvrRpv3.1 locus induce cell death in plants carrying Rpv3.1. (10 days post-agroinfiltration)