Chromosome-Level Genome Assembly Unveils the Molecular Mechanisms Underlying Disease Resistance in Ulmus parvifolia

Abstract

The absence of a comprehensive genome assembly for Ulmus parvifolia hinders advancements in scientific research and practical breeding efforts, ultimately affecting the cultivation of elm varieties with enhanced resistance to diseases. In this study, we presented a high-quality chromosome-level genome assembly of U. parvifolia by integrating various sequencing approaches. We discovered that the U. parvifolia genome is more than twice the size of Ulmus americana, primarily due to the large-scale amplification of long terminal repeat (LTR) retrotransposons. Phylogenetic analysis positioned U. parvifolia in a closer evolutionary relationship with Moraceae, followed by Cannabaceae, Rhamnaceae, and Rosaceae. 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. Chromosomal evolution analysis indicated a possible whole-genome triplication event in the evolutionary history of U. parvifolia. To study the differing susceptibility of U. parvifolia and U. americana to Dutch elm disease, we inoculated both elms with Ceratocystis ulmi and performed comparative transcriptomes analyses at 48, 96, and 144 hours post-inoculation. The results showed that several plant defense and immune response pathways were more highly expressed in U. parvifolia at 48 and 96 hours post-inoculation, implying a potential genetic basis for its higher resistance to Dutch elm disease. Our study represents an advancement in the genomic understanding of U. parvifolia, and especially sheds light on the genetic underpinnings of disease resistance in elms, and provides a foundation for future research into elm breeding for disease resistance and conservation efforts.