Genome and transcriptome analysis to reveal adaptation to new environments and hosts
L. GAGNEVIN (1), B. Roux (2), S. Bolot (2), S. Carrère (2), E. Charbit (3), S. Cunnac (4), M. A. Jacques (3), L. D. Noël (5), M. Arlat (6), R. Koebnik (4). (1) UMR PVBMT, CIRAD, Saint-Pierre, La Réunion, France; (2) Laboratoire des Interactions Plantes Micro-organismes (LIPM), INRA, UMR 441, Castanet-Tolosan, France; (3) UMR1345 IRHS, INRA, Beaucouzé, France; (4) UMR186 RPB, IRD, Montpellier, France; (5) Lab
Pathovars of <i>Xanthomonas</i> are interesting working models for the analysis of mechanisms of adaptation and specialization to hosts, plant tissues, niches and environments. The understanding of such mechanisms is important on practical and academic points of view since they can help explain how emergence of new diseases or of diseases in new situations may occur. Four research groups belonging to the <i>French Network on Xanthomonas</i> (FNX) have recently focused on genome and transcriptome sequencing of several pathovars of <i>Xanthomonas</i> chosen for their adaptation particularities, in a project called “Xanthomix”. <i>Xanthomonas</i> strains attacking Anacardiaceae, citrus, crucifers, legumes or rice were selected to help understand adaptation processes: genetic structure revealing either convergence or divergence for causing a specific disease on a specific host ; host tissue specialization (xylem vs. mesophyll) ; virulence variation (broad vs. narrow host range); contrasted epidemic situation (endemic vs. epidemic). RNAseq experiments were performed on a large set of strains to determine the extent and the diversity of the hrp regulon. In addition, the RNAseq dataset is also being used to improve <i>Xanthomonas</i> genome annotation and gene prediction. Analysis of transcripts allowed us to scan for unknown specific and non-specific effectors as well as small non-coding RNAs and hypothesize new mechanisms that could be involved in adaptation to host and environment.
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