Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in subgenus (Fungi, Ascomycota, Hypocreales).

Various strains of the mycoparasitic fungal species are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between and plant pathogenic fungi. Here, we determined the genome sequences of 11 strains, representing five species in subgenus , and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains ( ≤ .05) in the subgenus lineage. This was accompanied with gene copy number increases ( ≤ .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the genome included expansions ( ≤ .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter gene in was induced ( ≤ .009) by exposure to the antifungal mycotoxin zearalenone (1121-fold) and various fungicides. Deletion of resulted in mutants with reduced ( < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites in subgenus .