Chromosome-level genome assembly of Ulmus parvifolia identifies genomic signatures and transcriptional profiling underlying Dutch elm disease resistance

The lack of a high-quality Ulmus parvifolia genome assembly has impeded research on disease resistance and hindered breeding programs for resilient elm cultivars. In this study, we presented a chromosome-level genome assembly of U. parvifolia using integrated sequencing technologies. LTR retrotransposons, predominantly the Ty3/Gypsy Retand subfamily, underwent recent large-scale amplification, potentially contributing to the genome size of U. parvifolia. Phylogenetically, U. parvifolia is sister to a clade containing Moraceae, Cannabaceae, and Urticaceae. Notably, gene families associated with disease resistance and immune response were significantly expanded in U. parvifolia, pointing to an adaptive evolution to various biotic and abiotic stresses. To dissect differential susceptibility to Dutch elm disease, we inoculated U. parvifolia (resistant) and U. americana (susceptible) with Ceratocystis ulmi and performed comparative transcriptomics at 48, 96, and 144 h post-inoculation (hpi). Several plant defense and immune response pathways were markedly upregulated in U. parvifolia at 48/96 hpi, revealing a genetic basis for its enhanced resistance. This study advances genomic resources for elms, elucidates molecular mechanisms of disease resilience, and provides a foundation for breeding and conservation efforts.