3.7 Dickeya solani genomics revealed two vfmBalleles at balanced frequencies
We used a population genomic approach to investigate additional
ecological traits of the D. solani invading population. 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 ).
We also investigated the presence of the VfmBPro and
VfmBSer alleles in other Dickeya species. The
alignments of VfmB proteins retrieved from genomic databases revealed
the occurrence of the VfmBPro allele inD. dadantii , D. chrysanthemi and D. dianthicolagenomes, while the VfmBSer allele was found in D.
zeae genomes (Figure S6 ). However, the low number of genomes
available let open the possibility of the existence of additional
alleles in each of these Dickeya species.