Evaluation of different RNA extraction methods for high-quality total RNA and mRNA from Erwinia amylovora in planta

Obtaining a sufficient quantity of high-quality, intact RNA is the first crucial step in its study by RNA sequencing on next-generation sequencing platforms or quantitative PCR. Different RNA extraction methods or commercial kits vary in yield and in the quality and integrity of the RNA obtained, which may affect the results of downstream applications. Often, these factors depend on the organism under study and nature of the sample. Therefore, the selection of an appropriate RNA isolation method is critical. In this study, we present the results of an evaluation of three different commercial kits for the isolation of total RNA from Erwinia amylovora in apple tissue as well as the usefulness of different kinds of Deoxyribonuclease I for DNA removal and kits for rRNA depletion. To our knowledge, this is the first report on the method of isolation of high-quality E. amylovora mRNA for RNA-seq.