Estratégias de bioinformática no estudo da patogenômica de bactérias do gênero Xanthomonas

Abstract

The Xanthomonas genus comprises Gram-negative bacteria species, many of which are phytopathogens of plants with high economic value. With the advent of next generation sequencing (NGS), the increase in the availability of genomic data allowed the identification, through bioinformatics analysis, of many molecular features that grant to these organisms the ability to infect their host. In the present thesis, constituted by three sub-projects presented in the form of papers, different applications of bioinformatics strategies are described regarding the study of the genome-pathogenesis relationship (pathogenomics), in the context of the study of this genus. The first paper describes a pangenomic analysis of the species X. oryzae, which has as preferential host rice (O.sativa). This species comprises two distinct pathovars, oryzae and oryzicola, each one responsible to a specific disease and with a specific infection dynamic and symptomatology. Through the analysis performed based on the core genome of these pathovars it was possible to identify differentially distributed genes among them, some of which are directly associated with the pathogenesis process, such as those associated with the nutrient uptake, the CRISPR system and cell wall degradation. In the second paper we describe the development of a new tool for the analysis of genes from the TALE family, which are widely distributed in the Xanthomonas genus and are able to regulate the gene expression in the host. The tool is able to identify, based on a unannotated genome, the genes that code for proteins of the family and their respective targets on the genome of different plants. Finally, the third paper describes the sequencing of a local strain, obtained in Rio Grande do Sul (Brazil), of X. fuscans, derived from beans samples (Phaseolus vulgaris). The analysis of the genome of this strain showed many new virulence factors and functional and structural features when comparing to the reference strains for this species. Therefore, based on the analysis approaches and the proposed tool it was possible to identify new genomic features relevant in the study of the pathogenomics of different strains of Xanthomonas, and also provide a new tool to the study of genes associates with the pathogenesis of these bacteria and those with promising biotechnological potential.