Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1

African Xanthomonas oryzae pv. oryzae strains seem most closely related to and share several genetic features with pathovar oryzicola despite causing symptoms of bacterial leaf blight. The ability of most Xanthomonas plant pathogenic bacteria to infect their host relies on the action of a specific family of type III effectors called the TAL effectors. These microbial transcription factors are injected into the plant and manipulate the host transcriptome upon binding to the promoters of plant genes. The genes whose induction is of benefit to the pathogen are called susceptibility genes. RNA profiling experiments in rice using the Malian Xoo strain MAI1 and in silico prediction of TAL effector binding sites were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. RNAseq libraries (paired-end strand specific TruSeq Illumina) were constructed from RNA extracted from leaf tissues of Nipponbare plants collected 24 hours post inoculation with the Xoo strain MAI1 and a water control. Libraries were sequenced in a HiSeq2000 machine (Illumina) at the INRA Unité de Recherche en Génomique Végétale (Evry, France). Library quality was verified using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped against the rice genome (Nipponbare v. MSU7) using the Tuxedo suite v2.1.1 with the following parameters: Tophat (--max-multihits 20--b2-very-fast); Cufflinks (--frag-bias-correct --library-type fr-secondstrand --multi-read-correct); Cuffdiff (--upper-quartile-norm --multi-read-correc --FDR 0.05).