A comprehensive transcriptional landscape of Flavescence dorée phytoplasma infecting in field-grown Vitis vinifera leaves

RNA-Seq technology followed by three de novo assembly strategies was used to provide the first comprehensive transcriptomics landscape of flavescence dorée phytoplasma (FD) infecting in field-grown Vitis vinifera leaves. With an average of 8300 FD-mapped reads per library, we assembled 347 sequences, corresponding to 214 annotated genes, and identified 11 previously unannotated genes, 15 polycistronic transcripts and three genes supposedly localized in the gaps of the FD92 incomplete genome. Furthermore, we improved the annotation of 46 genes by the addition of 5’/3’ untranslated regions. Functional classification revealed that the most expressed genes were either related to transduction and protein biosynthesis or hypothetical proteins with unknown function. Some of the latter were predicted secreted proteins that could be bacterial effectors with a potential role in modulating the interaction with the host plant. Interestingly, qRT-PCR validation of the RNA-Seq expression values confirmed that a group II intron represented the FD genomic region with the highest expression values during grapevine infection. This mobile element may contribute to the genomic plasticity that is necessary for the phytoplasma to increase its fitness and endorse host-adaptive strategies. ur results provided new insights into the FD transcriptional organization and gene structure and may represent the starting point for the application of high-throughput sequencing technologies to study differential expression in FD and in other phytoplasmas with an unprecedented resolution.