Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight.

The aim of our study was to decipher differences in the response of a lowly virulent E. amylovora strain to infection of susceptible and resistant apple cultivars at the transcriptome level. For this purpose, we applied an RNA-seq technique to see the global changes in gene expression of E. amylovora while interacting with two apple cultivars at two time points after inoculation of shoots. Additionally, we compared transcriptomes of E. amylovora growing on a microbiological medium and in planta to elucidate transcriptional changes in bacterial cells induced by the host plant environment.