Insights into genomic evolution from the chromosomal and mitochondrial genomes of Ustilaginoidea virens

Abstract Ustilaginoidea virens , the causal agent of rice false smut, is an economically important filamentous fungal pathogen. A high-quality reference genome U. promotes understanding molecular mechanisms underlying its virulence and pathogenicity. Here, we report first chromosome-level assembly consisting seven chromosomes ranging from 2.4 to 7.5 Mb. The has dramatic improvements over previous assemblies, including considerably longer contigs, higher proportion repetitive elements more functionally annotated genes. Phylogenetic analyses revealed extremely low intraspecific sequence divergence in . By contrast, comparisons uncovered dynamic genomic alterations massive structural variations widespread lineage-specific regions (LSRs) among strains, which were mainly generated by recent burst retrotransposons. Genomic plasticity created LSRs might drive rapid evolution High-quality mitochondrial genomes eight strains exhibit size 94 102 kb. Consistently, contains conserved lengths exons highly mobile introns, contribute due gain/loss homing endonuclease This study highlights unique characteristics nuclear provides new insights into