3.8 VfmBSer strains were more aggressive than
VfmBPro strains in soft-rot assays
The modeling of the D. solani VfmBPro and
VfmBSer protein structures predicted a conformational
difference in the beta-sheet structure of the virulence regulator VfmB
(Figure 7a ). This change is explained by the exceptional
conformational rigidity of proline that strongly affects secondary
structures such as alpha helices and beta sheets. The modeling data
prompted us to test whether
VfmBPro-VfmBSer variation could be
associated with a change in aggressiveness. To compare the
aggressiveness of D. solani VfmBSer and
VfmBPro isolates, we used genomic data to identify a set
of 8 isolates carrying either VfmBPro (IPO2222, MIE35,
AM3a and 3337) or VfmBSer (Ds0432.1, RNS10-27-2A, Sp1a
and M21a), in which the other variations were at different positions
(Tables S3 and S4 ). Soft-rot assays using 10 inoculated potato
tubers per strain revealed that the set of the VfmBSerstrains was more aggressive (Kruskal-Wallis test; k=9.5; DF=1; p= 2 x
10-3) than that of the VfmBPro strains
(Figure 7b ).
To test the existence of differential expression of virulence genes in
tuber tissues, we compared transcriptomes of D. solani IPO2222
(VfmBPro) and Ds0432.1 (VfmBSer)
(Figure 7c ; Table S6 ). The expression of four genes
found differentially expressed based on transcriptomics (pelE ,impC , cytA and budA ) was further investigated by
RT-qPCR in the same samples used for transcriptomics: they found to be
also upregulated (Figure S8 ). Overall, 170 differentially
expressed genes (adjusted p-value < 0.05 and absolute log2
fold change > 2) were identified by comparative
transcriptomics. Most of them (150 genes) were upregulated in Ds0432.1
carrying the VfmBSer allele (Table S7 ). We
studied more specifically 35 well-characterized D. solanivirulence genes (Raoul des Essarts et al., 2019). We observed an
enrichment of these virulence genes among the upregulated genes inD. solani Ds0432.1, while none of them was found among the
downregulated genes (Table S8 ). These upregulated virulence
genes in D. solani Ds0432.1 included the pectate lyase genespelB, pelC, pelD, pelE and pelL, the protease genesptrA , prtB and prtC, and the T6SS-related
toxin/antitoxin genes hcp (Table S8 ). These upregulated
genes encompassed virulence determinants that are already known to be
regulated by the Vfm quorum-sensing in D. dadantii (Nasser et
al., 2013).