Gene expression changes of Pseudomonas syringae pv. actinidiae biovar 6 in various culture conditions

Pseudomonas syringae pv. actinidiae biovar 6 (Psa6) is a causal agent of kiwifruit bacterial canker and is a unique plant pathogenic bacterium, producing two types of phytotoxins, coronatine and phaseolotoxin. We investigated the expression behavior of virulent genes of Psa6 under various culture conditions. Two milliliters of bacterial resuspension (in each medium) were inoculated into 15 mL of respective test media and the cultures were shaken at 160 rpm at 27 or 18 °C. As test media, HS medium and HSC medium were used. HS and HSC media have been reported to activate coronatine production of Pseudomonas syringae pv. glycinea. Additionally, it has been reported that cultures at 18 °C, compared to 27 °C, induce the production of phytotoxins such as coronatine and phaseolotoxin. After incubation at 3 h, 1 mL of each culture was taken and used for RNA-Seq. Sequence data by IonPGM sequencer were assembled and analyzed using the CLC Genomics Workbench and the statistical software R with various packages (edgeR, limma, and gplots). Namely, using high-quality sequence reads with the reference genome of Psa6 MAFF 212134 (accession no. MSBW00000000), the reads per kilobase of exon per million mapped reads (RPKM) values were obtained and normalized. Then, using R software, the gene expression values relative to the 27 °C HS medium were calculated to log2 values of fold change (log2FC) with FDR (false discovery rate) values under the four culture conditions.