Comparative genomics of Eastern-Indian Ustilaginoidea virens strain NRRI-FSM-1 at whole-genome level unravels genome evolution and genetic plasticity.

Abstract

Introduction: Rice false smut (RFS), caused by Ustilaginoidea virens (teleomorph: Villosiclava virens), has emerged as a major global threat to rice production, causing reductions in yield, grain quality, and market value. Although first reported in India in the 1870s, genomic resources for this pathogen remain limited, constraining efforts toward understanding pathogen diversity and developing effective disease management strategies.

Methods: In the present study, a high-quality whole-genome sequence of the Eastern Indian U. virens isolate NRRI-FSM-1 was generated and analyzed. Comparative whole-genome sequence (WGS) analysis was further performed using six U. virens strains to investigate genomic diversity, structural variation, and candidate pathogenicity-related features.

Results: The assembled NRRI-FSM-1 genome was 36.3 Mb in size, comprising 985 scaffolds with an N50 of 5,781,932 bp. A total of 328,782 variants were identified, including 302,430 SNPs, 13,224 insertions, and 13,128 deletions. Additionally, 5,977 simple sequence repeats (SSRs) and 9,257 protein-coding genes were identified, representing the highest number of predicted genes reported so far among false smut genomes. Comparative genomics revealed substantial genomic diversity among the six strains, including variation in candidate effector repertoires, gene content, and population structure at both global and intra-Indian levels. Notably, significant diversity was observed among Indian strains, indicating considerable genomic variation across geographical regions.

Discussion: These findings expand the pathogenomic resource base for U. virens in India and globally, and provide insights into genome evolution and genetic plasticity in this important rice pathogen. The generated genomic resource establishes a foundation for future studies on pathogen surveillance, virulence mechanisms, and molecular breeding strategies for rice false smut management.