Chromosome-scale genome assembly and characterization of Saccharomycopsis schoenii, a necrotrophic predatory yeast

The necrotrophic predatory yeast Saccharomycopsis schoenii preys on diverse fungal species including multidrug-resistant Candida auris, making it a promising candidate for fungal biocontrol. Despite growing interest in its predation mechanisms, a high-quality reference genome is lacking. We constructed a chromosome-scale genome assembly of S. schoenii using a hybrid approach combining Pacific Biosciences HiFi long-read sequencing with Hi-C chromatin conformation capture. The 14.3 Mb genome is resolved into 6 nuclear and 1 mitochondrial chromosome, demonstrating high contiguity and near-complete gene-space representation. Building upon this reference, we generated an evidence-guided annotation using BRAKER2 and eggNOG-mapper to identify genes and other genomic features. Interestingly, this complete assembly also reveals an expanded mating-type (MAT) system with multiple active copies that are co-transcribed, bypassing conventional silencing mechanisms. Furthermore, comparative genomics highlights species-specific expansions in several gene classes; including, secreted aspartic proteases and adhesins, linked to its necrotrophic lifestyle. This improved reference genome provides a crucial resource for investigating the molecular basis of fungal predation and mating-type evolution.