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

Abstract

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.

Pedro Vilanova

Research Collaborator

I am a biologist with a Master’s in Genetics and Plant Breeding, working with a strong focus on New Generation Sequencing (NGS) applied to fungal genomics. My research focuses on understanding how fungal genomes function and how gene expression is regulated, with an emphasis on host–pathogen interactions and molecular adaptation.

Claudia Barros Monteiro-Vitorello

Principal Investigator

Associate Professor at ESALQ-USP specializing in molecular and microbial genetics. Her research focuses on plant-pathogen interactions, particularly in sugarcane, as well as microbial genomics and genome evolution.