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Unraveling the genomics of adaptation of Colletotrichum kahawae to Coffea arabica
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Resumo(s)
Fungi are one of the most destructive groups of plant pathogens, being responsible for more than 30 % of the emerging diseases worldwide. Colletotrichum kahawae is the causal agent of Coffee berry disease, one of the most devastating diseases of Coffea arabica in Africa. This pathogen is able to specifically infect green coffee berries, leading to severe production losses if no control measures are applied. In this thesis, we used an integrative approach, joining population genomics, pathology and gene expression, to better understand several aspects of this pathogen’s population dynamics and adaptation, including its evolutionary history, pathogenicity and aggressiveness. The population genomics analysis, revealed that C. kahawae is a true clonal pathogen, that probably emerged in Angola, quickly dispersed to East Africa, and only later colonized the Cameroon. Two clonal lineages within the Angolan population were detected and the evolutionary mechanism that gave rise to the Cameroonian population was not evident, leading to the proposal of alternative hypotheses. High genomic differentiation between C. kahawae and closely related species was detected, reinforcing its recognition as a distinct species. Further RAD-seq analysis uncovered the genomic loci putatively underlying C. kahawae’s pathogenicity. The annotation of these loci, suggest that several biological processes (detoxification, transport, signaling, and regulation of host and pathogen gene expression) could be involved in host infection. For testing association with aggressiveness, C. kahawae phenotypic profiling was performed and three different aggressiveness classes were created to accommodate all the variability observed. The genome-wide association analyses performed were able to detect a group of SNPs of small effect, providing candidate genes putatively associated with aggressiveness. Finally, aiming a follow-up validation of the functional role of candidate genes, the first steps to perform gene expression studies were followed. The best strategy to normalize a broad range of fungal and interaction samples in isolates with different aggressiveness profiles was established.
Descrição
Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2018
Palavras-chave
Teses de doutoramento - 2018