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Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

Domain theory has been developed as a mathematical theory of computation and to give a denotational semantics to programming languages. It helps us to fix the meaning of language concepts, to understand how programs behave and to reason about programs. At the same time it serves as a great theory to model various algebraic effects such as non-determinism, partial functions, side effects and numerous other forms of computation. In the present paper, we present a general framework to construct algebraic effects in domain theory, where our domains are DCPOs: directed complete partial orders. We first describe so called DCPO algebras for a signature, where the signature specifies the operations on the DCPO and the inequational theory they obey. This provides a method to represent various algebraic effects, like partiality. We then show that initial DCPO algebras exist by defining them as so called Quotient Inductive-Inductive Types (QIITs), known from homotopy type theory. A quotient inductive-inductive type allows one to simultaneously define an inductive type and an inductive relation on that type, together with equations on the type. We illustrate our approach by showing that several well-known constructions of DCPOs fit our framework: coalesced sums, smash products and free DCPOs (partiality and power domains). Our work makes use of various features of homotopy type theory and is formalized in Cubical Agda.