Exploring the Distribution of Secondary Metabolite Gene Clusters in the Fungal Genus Alternaria and Closely Related Taxa
Alternaria species produce a variety of secondary metabolites (SMs), which are important emerging phytotoxins and mycotoxins. Recent studies have revealed surprising diversity in the SM-encoding biosynthetic gene cluster (BGC) profiles of fungi, yet little is known about the toxicological potential of Alternaria, reflected by the lack of effective surveillance and management regulations. In this thesis, the distribution of BGCs was explored both across the Alternaria phylogeny, and within individual genomes. BGC profiles, especially those of the polyketide synthase class, were found to closely match phylogenomic patterns (Chapter 1). Case studies on the presence/absence patterns and architecture of the alternariol BGC across all strains (Chapter 2), and the BGC profile of Alternaria sect. Infectoriae strains (Chapter 3) are presented. Finally, the distribution of all BGCs within individual genomes is investigated (Chapter 4), with focus on genome compartmentalization. These results can inform management practices to mitigate the impact of fungal disease.