Crispr Systems in Plant Pathogens: A New Tool for Epidemiological Surveillance

Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. The widely distributed CRISPR loci consist of highly conserved DNA repeats that are interspersed by unique, similarly sized spacers which originate from previous attacks by viruses and/or plasmids. For efficient management of plant diseases, knowledge about the pathogen's population structure and tools for epidemiological surveillance are prerequisite. We wish to exploit CRISPR loci as a molecular typing tool of plant pathogens, as exemplified by Xanthomonas, an important clade of Gramnegative bacteria infecting a plethora of plants, including rice, cereals, cassava, banana and citrus fruits. CRISPR loci of 56 X. citri subsp. citri strains of world-wide origin were sequenced, revealing a repertoire of 37 unique spacers. A dendrogram based on the presence and absence of spacers was largely congruent with previous typing using AFLP. Our results demonstrate that CRISPR-based spoligotyping can be used as an efficient and robust method to study the phylogenetic relationships among isolates of plantpathogenic xanthomonads, such as the citrus cancer pathogen X. citri subsp. citri. Implementation of Xanthomonas spoligotyping will serve phytosanitary measures by assisting the epidemiological surveillance of outbreaks of citrus canker and other diseases. (Texte integral)