A Near-T2T Genome Assembly of Elsinoe fawcettii Provides Insights into Host Adaptation Driven by Cis-Regulatory Evolution

<i>Elsinoe fawcettii</i> is a devastating citrus pathogen worldwide, yet high-quality genomic resources are lacking, limiting insights into its adaptive mechanisms. Seventeen strains collected from 13 host species across 5 Chinese provinces were confirmed as <i>E. fawcettii</i> by multi-loci (ITS, <i>rpb2</i>, <i>tef</i><i>1-α</i>) phylogenetic and morphological analyses. A near-telomere-to-telomere (near-T2T) genome for representative strain FJ-Y-3 was constructed using integrated PacBio and Hi-C sequencing. The 24.40 Mb assembly was organized into 11 chromosomes with exceptional completeness (BUSCO: 97.1%) and continuity (scaffold N50: 2.18 Mb). Pan-genome analysis revealed a closed structure, with core genes representing 77.19% of the total, suggesting evolutionary adaptation through fine-regulation of conserved elements rather than extensive gene content variation. Accessory genes were significantly enriched in terpenoid/polyketide metabolism, cell surface remodeling, and xenobiotic degradation, underscoring metabolic plasticity. Whole-genome resequencing showed single-nucleotide polymorphisms as the dominant variant, with ~60% residing in regulatory regions, implicating cis-regulation as a key adaptive mechanism. This work provides a high-quality genome and multi-omics framework for <i>E. fawcettii</i>, establishing a crucial molecular foundation for understanding pathogen adaptation and developing sustainable disease management strategies.