Temporal transcriptomic profiling of Colletotrichum lindemuthianum race 65 during compatible and incompatible interaction with common bean

Abstract

Anthracnose, caused by Colletotrichum lindemuthianum, is one of the most severe diseases affecting common bean (Phaseolus vulgaris), leading to significant yield losses in major production regions. Since this pathogen is characterized by high variability and a remarkable ability to overcome plant defense mechanisms, understanding the infection process at the molecular level is essential for developing more effective and durable control strategies. In this context, the present study aimed to investigate the molecular basis of the infection process caused by race 65 of the pathogen in contrasting bean genotypes (Ouro Vermelho, resistant, and BRS Estilo, susceptible) through a time-series analysis of the fungal transcriptome (0, 48 and 96 hpi) using RNA-seq. The identification and characterization of differentially expressed genes, combined with the analysis of functional categories essential for pathogenicity, enabled inferences about the adaptive strategies employed by the fungus during the infection process. The prediction of secreted proteins revealed the presence of six and seven CAZymes in the Inter A and Inter V groups, respectively, at 96 hpi, with a predominance of enzymes belonging to the glycosyl hydrolase (GH) class. Among the 21 transport-related proteins identified, heat shock proteins (HSPs) and MFS transporters were particularly prominent, especially within the Inter V subset (96 hpi). In addition, 15 Candidate Secreted Effector Proteins (CSEPs) were detected, three of which showed significant similarity to proteins recorded in the PHI-base database. Overall, these results provide molecular insights into the pathogenicity of C. lindemuthianum and highlight potential targets for breeding strategies aimed at achieving durable resistance to anthracnose in common bean.