Multi-locus phylogenetic network analysis ofAmpelomycesmycoparasites isolated from diverse powdery mildews in Australia and the generation of twode novogenome assemblies

The interactions between powdery mildews (Ascomycota,Erysiphaceae), obligate biotrophic pathogens of many plants, and pycnidial fungi belonging to the genusAmpelomyces, are classic examples of specific mycoparasitic relationships. These interactions are common and finely tuned tritrophic relationships amongst host plants, powdery mildews, andAmpelomycesmycoparasites wherever these organisms co-occur in the field. SelectedAmpelomycesstrains have already been developed as biocontrol agents of powdery mildew infections of some crops. In Australia, their study has received little attention so far. Only a singleAmpelomycesstrain, included in a whole-genome sequencing (WGS) project, was known from this continent. Here, we report the isolation of 20 moreAmpelomycesstrains from eight powdery mildew species in Australia. Multi-locus phylogenetic network analyses of all the 21 AustralianAmpelomycesstrains carried out in combination with 32 reference strains from overseas revealed that the Australian strains belonged to four molecular taxonomic units (MOTUs). All those MOTUs were delimited earlier based onAmpelomycesstrains isolated in Europe, North America, and elsewhere. Analyses indicated possible recombination events amongst phylogenetically differentAmpelomycesstrains. Based on the phylogenetic analyses, two Australian strains belonging to different MOTUs were selected for WGS. Long-read (minION) and short-read (Illumina) technologies were used to provide genome assemblies with high completeness. Both assemblies reported here had bipartite structure, i.e., consisted of AT-rich, gene-sparse regions interspersed with GC-balanced, gene-rich regions. These new high-quality assemblies and evidence-based annotations are important resources for future analyses of mycoparasitic interactions to disentangle molecular mechanisms underlying mycoparasitism, possible new biocontrol applications, and natural tritrophic relationships.