The Genome Sequence Of The Banana Black Sigatoka Pathogen Mycosphaerella fijiensis Reveals An Extraordinary Species Specific Expansion and Is Applied To Analyze Avirulence and Fungicide Resistance

Mycosphaerella fijiensis is a hemibiotrophic fungal pathogen and the causal agent of the devastating black Sigatoka or leaf streak disease of banana (BLSD). Control of this disease requires weekly applications of fungicides in most cultivation areas with concomitant negative effects on humans and wildlife in precarious tropical environments. Major problems for disease management are the rapid development of fungicide resistance within populations of the pathogen and the lack of effective genes for resistance in commonly grown clones of banana. To develop tools for molecular analysis and to identify genes involved in host-pathogen interactions, a new genetic map was made and used to facilitate assembly of its genomic sequence. Comparisons with related plant-pathogenic fungi revealed that the genome of M. fijiensis at 74 Mb is greatly expanded mostly due to the presence of LTR retrotransposons, making it the largest ascomycete genome sequenced to date. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex on banana, M. eumusae and M. musicola, also are expanded. Electrophoretic karyotypes and analyses of molecular markers in populations of M. fijiensis in Costa Rica identified extraordinarily high levels of variation including numerous chromosome-length polymorphisms. Dramatic differences in the frequencies of fungicide resistance in sprayed versus an unsprayed field showed how rapidly allele frequencies can change, presumably due to selection in sexually recombining populations. Analysis of the predicted gene models identified MfAvr4, which is similar to a gene that encodes an effector in the tomato pathogen Cladosporium fulvum. Infiltration of purified MfAvr4 protein into the leaves of a resistant and susceptible banana cultivar resulted in a hypersensitive response in the former, indicating the presence of a homologue of the tomato Cf4 resistance gene in banana. Availability of the M. fijiensis genome sequence will facilitate the identification of its pathogenicity factors as well as understanding fungicide resistance and genome evolution.