Data were scanned according to manufacturer specifications.
Hybridizations were with Genechip Hybridization Oven 640 and Genechip Scanner 3000 7G from Affymetrix
nucleic acid labeling protocol
Labeling was carried out using Genechip 3ﾴIVT Express Kit from Affymetrix
growth protocol_L. japonicus/P. syringae
Seeds of L. japonicus MG-20 and Gifu B-129 seeds were treated with concentrated sulfuric acid for 2 min., rinsed ten times with sterile distilled water and germinated in Petri dishes containing agar/water (0.8%). Seedlings were transferred to sand-perlite soil mix (1:1) and cultivated in growth chamber with a 16h day/8h night photoperiod (photon flux density of 200 ?mol m sﾖ1 provided by cool-white fluorescent lamps) and 24/21 ﾱ 2ﾰC and 55/ 65 ﾱ 5% day/night temperature and relative humidity, respectively. Plants were regularly irrigated with half-strength Hoaglandﾒs nutrient solution. Three week-old L. japonicus plants (with 6 to 8 true leaves) were used in all experiments. Pto inocula were prepared by growing bacteria in Kingﾒs B agar-medium plates at 28ﾰC for 48 h and scraping cells off in 10 mM MgCl2, pH 7.0, to a cell density of 0.1 A600.
Four central leaflets per plant were infiltrated with a bacterial suspension using a needleless 1-ml syringe. Mocked-inoculated controls were infiltrated with 10 mM MgCl2. 4 leaflets per plant were harvested at 24 hpi (inoculated with Pto or MgCl2), each treatment consisting of 24 plants. Leaflets from all 24 plants with the same treatment were pooled, frozen in liquid nitrogen and stored at -80ﾺC. This pool represented one biological replicate. Overall, there were 3 biological replicates corresponding to 3 independent experiments performed with a 2-week interval.
RNA extraction protocol
Total RNA were extracted from frozen tissues using SpectrumTM Plant Total RNA kit (Sigma-Aldrich) according to the manufacturerﾒs instructions.