Comparative Genomic Analyses of Colletotrichum lindemuthianum Pathotypes with Different Virulence Levels and Lifestyles

<i>Colletotrichum lindemuthianum</i> is the most frequent pathogenic fungus of the common bean <i>Phaseolus vulgaris</i>. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many <i>Colletotrichum</i> species. Due to host-pathogen coevolution, <i>C. lindemuthianum</i> includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among <i>C. lindemuthianum</i> pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions.