, results was performed using Fisher's exact test

, Total RNAs were purified by extraction in a guanidinium isothiocyanate extraction buffer and 5 recovery by centrifugation on a caesium chloride cushion as described in, vol.17

, Transcriptome CATMA array hybridization

, Transcriptome profiling was carried out at the URGV -Plant Genomics Research

, France) using Arabidopsis CATMA arrays containing 24,576 gene-specific tags, vol.37

, For 13 each sample, cRNAs were synthesized from 2 µg of total RNA using the Message Amp 14 aRNA kit (Ambion, www.ambion.com), and 5 µg of cRNA was reverse transcribed using 300 15 units of SuperScript II (Invitrogen) and Cy3-dUTP or

, Labelled samples were combined, purified and concentrated using YM30 Microcon columns 17 (Millipore). The hybridization of labelled samples to the slides and the scanning of the slides

, Transcriptome statistical analysis was based on dye swaps (i.e. two arrays each containing 21 24,576 GSTs and 384 controls). For each array, the raw data consisted of the log2 median 22 feature pixel intensity without background subtraction at 635 nm (red)

, GSE11793) and at CATdb (project RA06-04_BOS1) according to the "Minimum Information

S. Table, Primer efficiency 5 (E) for qPCR was calculated from standard curve slope according to E =

S. Table, List of total Arabidopsis genes modulated during D. dadantii infection 12 or 24

, When 9 p-value were higher than 0.05, fold change ratios were shaded in light grey. Red scale bar: up-10 regulated genes; green scale bar: down-regulated genes. The threshold for modulated genes

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, A: Venn-diagram of up and down-regulated genes 12 and 24 hours post-inoculation 4 (hpi). B: functional classification of the 61 genes up-regulated both 12 and 24 hpi

, Tryptophan (Trp) and indole glucosinolate (IG) metabolic pathways. All Trp and 6 IG metabolism-related genes in black are up, vol.2

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, Upon tissue disruption by chewing insects or 11 macergenic pathogens, the action of hydrolases leads to the production of various highly toxic 12 and instable breakdown products (simple nitrile, epithionitrile, thyocyanate)

, Fig 3. Transcriptome validation by qRT-PCR. Transcript accumulation of representative

J. Trp, D. Genes-after, and . Dadantii, A) or buffer (B) inoculation was analysed by 16 qRT-PCR. Fold changes were normalised to 0 hpi for each gene (set to one)

, Transcript 19 accumulation of two representative IG biosynthesis genes CYP79B2 (A) and SOT16 (B) was 20 analysed by qRT-PCR 24 hours after D. dadantii inoculation on Col-0 wild type Arabidopsis 21 and mutants impaired in JA biosynthesis (jar1) or impaired in JA sensitivity (coi1). Fold 22 changes were normalised to 0 hpi for each Arabidopsis genotype

, A) and SOT16 (B) and of two representative JA biosynthesis genes LOX2, genes, vol.79, issue.2

C. , OPR3 (D) was analysed by qRT-PCR. Inoculations were performed with buffer 5 inoculation, D. dadantii wild type strain (3937) and mutants altered in bacterial protein 6 secretion systems inoculation (prtE type I, outC type II and hrcC type III) on Col-0 wild type

. Arabidopsis, Fold changes were normalised to 0 hpi for each inoculation condition (set to 8 one). Error bars show the experimental values of the two biological repeats

, Fig 6 Effect of a ?pel mutation altering the five major pectate lyases synthesis on IG and 10 JA biosynthesis induction. Expression of CYP79B2 and SOT16 IG biosynthesis genes, and 11 LOX2 and OPR3 JA biosynthesis genes was analysed by qRT-PCR after infection by D

, Symptoms were scored during five 17 days post inoculation on Col-0 and mutants using the following symptom severity scale: 0 = 18 no symptom, 1 = maceration restricted to the site of inoculation, 2 = maceration extending 19 from the site of inoculation, 3 = maceration covering the whole leaf (C). * and ? indicate that 20 score frequency of the highest degree of symptom (scored 3) and of plant with no symptom 21 (scored 0) respectively are statistically different from the wild type one (Fisher's exact test, 22 two sided p-value < 0.05), dadantii (3937) wild type strain and the ?pel mutant impaired in the synthesis of the five 13 major pectate lyases PelABCDE