With the advent of next-generation sequencing technologies, recent works have revealed that the genomes of plant pathogenic fungi are very plastic and dynamic and encode several hundred of putative effectors as well as proteins related to the metabolism of carbohydrates, production of toxins and secondary metabolites. This plasticity is usually associated with the presence of transposable elements and/or "dispensable" chromosomes, which carry a set of pathogenicity-related genes and also determine the pathogens' capacity of infecting different organs and hosts. In addition to the incontestable economic importance of the cacao pathogens Moniliophthora perniciosa and M. roreri, these fungi are very interesting models to study the genomic adaptations of plant pathogenic fungi. Particularly, the biotypes C and S of M. perniciosa have similar characteristics related to the disease development, but differ in their host range (they infect species of the genus Theobroma and Solanum, respectively). In this regard, comparative genomics can give insights into the mechanisms that led to the capacity of these biotypes to exploit different host plants. Furthermore, the comparison of the genomes of M. perniciosa and M. roreri might point to the differences related to M. perniciosa capacity of infecting different plant organs (stems, flower cushions and fruits) as well as to the similarities associated with their ability of infecting fruits. Overall, this comparative genomic study will give insightful glimpses into the different pathogenic strategies adopted by plant pathogens, and it will certainly help to identify the genomic characteristics (transposable elements, dispensable chromosomes) that favored the modeling of the genomes of these economically important fungi. On the basis of the expected results, this work will certainly bring central contributions to the current knowledge on plant-pathogen interactions.
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