Transcriptomic analysis of Erwinia amylovora during colonization on trichomes of apple

In this study, we aimed to identify differentially expressed genes in the fire blight pathogen Erwinia amylovora during colonization on trichomes of apple. E. amylovora strain Ea110 was dip-inoculated onto apple leaves (Malus domestica, cultivar McIntosh) in an apple orchard. Glandular trichomes and non-glandular trichomes were collected from the inoculated leaves 3 days post inoculation. E. amylovora was collected from the trichomes through vortexing and sonicating, followed by the RNA isolation. Sequencing was performed on Illumina Novaseq. Differentially expressed genes were identified as compared to the original E. amylovora inoculum in phosphate buffer saline, from an overnight culture of E. amylovora in LB broth.