RNA-Seq of potato plants reveals a complex of new latent bacterial plant pathogens

The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in diagnostics of viruses and other plant pathogens. A transcriptome represents all RNA molecules, including the coding mRNAs as well as the noncoding rRNA, tRNA, etc. A distinct advantage of RNA-Seq is that cDNA fragments are directly sequenced and the reads can be compared to available reference genome sequences. This approach allows the simultaneous and hypothesis-free identification of all pathogens in the plant. We conducted surveys for potato (Solanum tuberosum L.) -associated phytopathogenic bacteria in 56 original and GenBank RNA-seq data sets for potato breeding material. Bacteria of genera Pseudomonas, Burkholderia, Ralstonia, Xanthomonas, Agrobacterium, and species of family Enterobacteriaceae were most frequently detected in RNA sets from the studied plants. RNA-seq reads identified as Xanthomonas spp. were within X. vesicatoria, and some other species. Xanthomonas spp. covered up to 9,1% of all reads and included the major clades of these bacteria known as pathogens of solanaceous crops, but potato. Bacteria of genus Xanthomonas infect different plant species under artificial inoculation, suggesting that they are shared among wild plants and crops. Our studies indicated that a larger number of solanaceous plants can be occupied by specific Xanthomonas pathovars as endophytes or latent pathogens. Revealing bacteria distribution in the plant breeding material using RNA-seq data improves our knowledge on the ecology of plant pathogens. © Published under licence by IOP Publishing Ltd.