Transcriptome Analysis Uncovers the Gene Expression Profile of Hemileia vastatrix (Race XXXIII) during the Interactions with Resistant and Susceptible Coffee

Coffee leaf rust is caused by Hemileia vastatrix Berk. and Broome and is the most important coffee disease in all regions where coffee is cultivated. Here, we sought to sequence the transcriptome of H. vastatrix race XXXIII to obtain a database for use as a reference in studies of the interaction between the fungus and coffee. In addition, we aimed to identify differentially expressed genes that have the potential to act as effector proteins during the interaction. Sequencing of cDNA libraries from uredospores and from compatible and incompatible interactions at different key time points generated about 162 million trimmed reads. We identified 3523 differentially expressed genes. The results suggested that the fungal transcriptome is dynamically altered over the course of infection and that the interaction with a susceptible plant upregulates a larger set of fungal genes than the interaction with a resistant plant. Co-expression network analysis allowed us to identify candidate genes with the same expression pattern as that of other effectors of H. vastatrix. Quantitative PCR analysis identified seven transcripts that may be effectors involved in the coffee-H. vastatrix interaction. This information provides a basis for obtaining new insights into the molecular mechanisms of infection in this pathosystem. Understanding gene expression during the infection process may contribute to elucidating the molecular mechanisms leading to the breakdown of resistance by new physiological races of the fungus.