Ferramentas para comparação genomica

Orientador : João Carlos SetubalTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Com o crescente número de genomas seqüenciados e publicados, surge a necessidade de se analisar as seqüências geradas, com o objetivo de se entender melhor caracterizações funcionais dos organismos estudados, assim como aspectos evolutivos. Um projeto genoma de um organismo, em especial de um procarioto, consiste essencialmente de três grandes fases: o seqüenciamento, a anotação e a análise. A última etapa, por sua vez, consiste na tentativa de se obter uma visão global do genoma a partir da anotação e a partir de outras análises, como por exemplo a comparação com outros genomas. E é nesse contexto, comparação de genomas, que esta tese se insere. Nosso trabalho propõe metodologias para comparação detalhada de dois genomas, tanto no nível de DNA, quanto no de seus genes, assim como a implementação dessas metodologias. O principal objetivo é fornecer ao usuário um conjunto de ferramentas para caracterização funcional do organismo estudado, servindo também como ferramental auxiliar na anotaçãoAbstract: With increasing availability of published genome sequences, we need to analyse them in order to understand functional and evolutionary issues of the organisms. A genome project, in particular for prokaryotes, consists of three main phases: sequencing, annotation and analysis. The last phase consists of getting an overview of the genome from the annotation and other analysis, like comparison to other genomes, for example. This thesis is about genome comparison. We propose methodologies for detailed comparison of two genomes, at the DNA and their genes levels. The main goal is to provide a set of tools for functional characterization of organisms, serving also as an auxiliar tool for annotationDoutoradoDoutor em Ciência da Computaçã

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses.

Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results: Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A?+?AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. Conclusions: Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes