Cytogenomic characterization of Colletotrichum kahawae, the causal agent of coffee berry disease, reveals diversity in minichromosome profiles and genome size expansion

Colletotrichum kahawae is an emerging fungal pathogen, which has recently undergone a speciation process from a generalistic ‘C. gloeosporioides species complex' background by acquiring the unique capacity to infect green coffee berries, thus causing coffee berry disease. This is a severe and widespread disease in Africa and an imminent threat to Arabica coffee cultivation in Asia and America, if the pathogen enters those continents. Genetic diversity within C. kahawae is low but notorious differences in pathogen aggressiveness have been described. This work characterized two cytogenomic traits (genome size and minichromosome profiles) of a collection of C. kahawae isolates, representing the breadth of its genetic diversity and distinct aggressiveness classes, along with closely related taxa. The results obtained constitute the first flow cytometry-based genome size estimation in the genus Colletotrichum and show a c. 8 Mb genome size expansion between C. kahawae (79·5 Mb on average) and its closest relatives (71·3 Mb), corroborating evidence indicating that C. kahawae (i.e. the coffee berry disease pathogens) should remain as a distinct species. Results have also shown the presence of two to five minichromosomes in C. kahawae, suggesting a positive relationship between the number of minichromosomes and the level of aggressiveness of the different isolates analysed, while no correlation could be established between aggressiveness and whole genome size. Overall, these results may be the basis for the identification of pathogenicity/aggressiveness-related factors in such minichromosomes, and may provide clues to the characterization of specific markers for aggressiveness classes.