Illumina HiSeq 2500 sequencing; RNA-seq of wheat leaves and roots in response to Xanthomonas translucens infection
RNA-seq of wheat leaves and roots in response to Xanthomonas translucens infection
Bacterial strains and plant inoculation The X. translucens type strain CFBP 2054 was used in this study. Bacteria were cultivated at 28°C in Peptone sucrose agar (PSA) medium.. Triticum aestivum cv. Chinese Spring plants were maintained in a growth chamber with cycles of 12 h of light at 21°C and 50% relative humidity (RH) and 12 h of dark at 21°C and 50% RH. Leaves of 49 days-old plants were infiltrated with a bacterial suspension in water with an optical density at 600 nm (OD600) of 0.5 using a needleless syringe. Plants inoculated with water were used as controls. For transcriptomic and proteomic analyses, leaves and root tissues were harvested 1 day post-inoculation (dpi), when symptoms were not visible yet. The infiltrated zone was collected as previously described (Reimers et al., 1991). Three biological replicates per treatment were performed, and each with pooled leaves from two independent plants per replicate. Once pulverized in liquid nitrogen, each sample was split into two aliquots, for protein and RNA extraction respectively.  RNA-seq transcriptome sequencing was performed on leaves and roots. Samples were ground to a fine powder in liquid nitrogen and total RNA was isolated (TRI Reagent® (MRC, Cincinnati, OH)) 25. Then, it was treated with DNase and RNA quality was confirmed with Experion™ Automated Electrophoresis System, Nanodrop™ and gel electrophoresis The preparation of mRNA libraries was done using the TrueSeq Stranded mRNA Sample Preparation kit (Illumina Inc., San Diego, CA). The library quality validation (concentration and length of DNA fragments) was performed by Fragment Analyzer using the standard and high sensitivity DNA kits (Agilent Technologies, Santa Clara, CA) and by qPCR (LightCycler 480; Roche Diagnostics, Meylan, France).
Experimental Factor: infect
none
Experimental Factor: organism part
root