3.6 The population genomic analysis of D. solaniidentified two alleles at the vfmB gene, at balanced frequencies
We studied SNPs and InDels in 76 D. solani genomes
(Figure S2 ), 56 of which were assembled after Illumina
sequencing in this study, while the 20 others had been previously
acquired using the same sequencing approach (Khayi et al., 2015). Out of
the 76 genomes, 66 exhibited from 2 to 11 SNPs and InDels when compared
to the D. solani 3337 reference genome (Figure S2 ). In
the nine others, more than 100 SNPs were observed: some of these SNPs
were clustered in regions of the chromosome (RNS13-30-1A, PPO9134,
PPO9019, RNS13-31-1A, RNS13-48-1A, RNS15-102-1A, RNS07-7-3B) while
others were distributed along the genome (RNS05-1-2A and RNS10-105-1A).
Focusing on the 66 genomes exhibiting less than 12 SNPs compared to the
strain 3337, 45 non-synonymous variations were identified in whole
genomes (Table S5) . Two-third of them (30 out of 45) were
private to a single genome, while the 15 others were found in at least
two genomes. Among these 15 later, three variations were identical in
four strains, two others in five strains and one was present in 19
genomes (Table S5 and Figure 6a) . The most balanced frequencies
alternated a thymine (T) in 19 genomes and a cytosine (C) residue in the
other 48 genomes at the position 2,930,940 in the reference D.
solani 3337 genome (Figure 6a ). The C to T modification caused
a proline (VfmBPro allele) to serine
(VfmBSer allele) change at the position 55 in the VfmB
protein. A SNP-based tree of these 67 strains (Figure 6b )
revealed that the D. solani isolates carrying
VfmBSer were placed in two different sub-clusters, one
with only two VfmBSer D. solani strains, EU3296
and Ds0432.1, and the other mainly VfmBSer strains.
The VfmBSer allele was present in 25% (19 out of 76) of
all analyzed D. solani genomes. A similar percentage (27%, 17
out of 63) was observed when only the French isolates were considered.
Using the isolation year of these 63 D. solani isolates, we drew
the dynamics of the percentage of the VfmBSer alleles,
which was found to fluctuate over the past decade (2005-2015) with a
peak in 2013-2014 (Figure 6c ).