Updated chromosome-level genome assembly of Sporisorium scitamineum with improved accuracy and completeness

In 2015, we published the complete genome assembly of Sporisorium scitamineum , the fungal pathogen responsible for sugarcane smut disease, generated from PacBio long-read sequencing and polished with Illumina short reads. Since then, the tools for genome assembly have improved considerably, including advances in sequencing technologies and bioinformatics workflows, motivating us to revisit our original assembly. Here, we present an updated genome version, using newly generated high-quality Illumina short-read data and DeepVariant-based polishing, resulting in corrections at approximately 5,500 genomic positions. BUSCO benchmarking in protein mode demonstrated increased genome completeness from the original 94.2% to 99.3%, indicating substantial improvements in both accuracy and gene annotation reliability. Additionally, comparison with publicly available assemblies reveals that most sequence polymorphisms occur in isolates belonging to the Asian lineage, consistent with earlier population-level studies. This enhanced genome assembly provides a significantly improved reference resource, enabling more robust genetic, evolutionary, and functional studies of this economically important sugarcane pathogen.