Résumé
Sequence data from the whole genomes of over 1000 organisms are currently available in the NCBI (National Center for Biotechnology Information) data base, including genomes of several viral and bacterial sugarcane pathogens. Genome sequences of sugarcane viruses have been extensively used to develop molecular diagnostic methods that are very efficient and useful for the identification and detection of these pathogens, and their control during movement of sugarcane germplasm. Furthermore, whole genome comparisons have improved our knowledge of molecular evolution and molecular ecology of sugarcane pathogens. For instance, sequencing and annotation of the genome of Xanthomonas albilineans revealed that this bacterial pathogen experienced genome reduction during its speciation. Additionally, this xanthomonad is notably missing the Hrp type III secretion system and the xanthan gene cluster that are commonly found in pathogenic Xanthomonas species. Transposon mutagenesis of X. albilineans resulted in the identification of new candidate fitness and pathogenicity factors that could be used to develop genetic-based control methods. The comparison of several isolates of Sugarcane yellow leaf virus (SCYLV) resulted in the identification of several genotypes of this virus which vary in their capacity to infect sugarcane cultivars. Knowing the genetic diversity of SCYLV in a given location is therefore important for efficient screening of resistant plant material. However, although several virus pathogens are already known and extensively studied, it is assumed that unknown pathogens are still to be discovered in sugarcane, especially if these pathogens do not cause symptoms that can be easily observed, such as SCYLV. Sequencing of unknown genomes will facilitate implementing of a new strategy of diagnostics, the so-called sequence-independent approach which aims at deciphering the virome (= the genomes of all the viruses that inhabit a particular organism). It is believed that this metagenomics approach will drastically improve routine quarantine diagnostics in the future and gather dozens, if not hundreds, of genome sequences that will eventually contribute to the understanding of the diversity and evolution of these pathogens, and the pathogenicity mechanisms used to cause disease. (Texte intégral)