3.6 Pectate lyases gene expression is higher in Dickeya solani than in D. dianthicola
The capacity of D. solani to initiate rotting with a low bacterial load suggested a differential expression of pectate lyase genes between the two species. To test this hypothesis, the expression levels of the pelA , pelD and pelE genes were quantified by RT-qPCR in the five D. solani and five D. dianthicola strains grown separately in a rich medium (in the absence of pectin) and in emerging lesions of potato stems and tubers (see a detailed protocol in SM2). The expression of two other virulence genes,cbsE and acsD, which are not involved in the plant cell wall degradation, but in iron-uptake, were also compared. Four RT-qPCR measurements were performed per condition and gene. For each gene, Kruskal-Wallis tests revealed differences between the six treatments (rich medium, stems and tubers for the two species, considering each strain as a replicate) for the different genes: pelA (k=17.1; DF=5 ; p=4x10-3), pelD (k=25.1; DF=5 ; p=1x10-4), pelE (k=24.9; DF=5; p=1x10-4), cbsE (k=20.3; DF=5 ; p=1x10-3) and acsD (k=21.3; DF=5; p=7x10-4).
Pairwise post-hoc Tukey tests were used to compare gene expression between D. solani and D. dianthicola . In the absence of pectin (Figure 5 ), the pelA (F=864.3; p< 10-11), pelD (F=864.3; p< 10-11) and pelE (F=2.9; p= 4 x 10-3) genes were expressed at a higher level inD. solani than in D. dianthicola . The expression levels of the cbsE (F=0.377; p=0.99) and acsD (F=-1.0; p=0.99) genes were not significantly different between species (Figure S6 ). In the absence of pectin, a higher expression of pectate lyase genes, especially pelE , could be considered as an advantage for initiating a rapid degradation of the plant cell wall polymers.
In symptomatic potato tubers and stems, some remarkable gene expression patters could be noticed (Figures 5 and S6 ). The expression levels of pelD and pelE were higher in D. solanithan in D. dianthicola (pelD : F=864.3; p< 10-11 in tubers and F=4.5; p= 10-4in stems; pelE : F=4.5; p= 1.1 x 10-4 in tubers and F=8.1; p < 10-11 in stems). ThepelA (F=864.3; p< 10-11) andcbsE (F=3.4; p= 0.01) genes were expressed at higher levels inD. solani than in D. dianthicola stem tissues, but not in tubers (pelA : F=-0.09; p=1 and cbsE : F=0.67; p=0.99). TheacsD expression level did not differed between the two species in diseased tubers (F=-1.5; p=0.9) and stems (F=0.5 p=0.9). Overall, in plant symptoms, D. solani maintained a higher expression of the virulence genes pelD and pelE compared to D. dianthicola .