Chromosome-level genome assembly and annotation of Ulmus minor reveal dynamic intrageneric clusters of resistance genes

The field elm (Ulmus minor) is an emblematic species of the European landscape, which has been severely affected by Dutch elm disease (DED) since the 20th century. To support restoration and conservation of this species and congeners, we present a de novo assembly and annotation of a wild genotype tested positive for DED resistance, along with a comprehensive phylogenetic analysis with related species. Cutting-edge sequencing technologies were used alongside high-throughput chromosome conformation capture technologies for chromosome conformation capture. Our assembly spans approximately 2.1 Gb, with scaffold and contig N50 sizes of 133.765 and 8.189 Mb, respectively. Repetitive elements account for 81.45% of the genome size. Using transcriptomic information from 19 tissues in varying developmental stages and gene model prediction techniques, a total of 46,357 protein-coding genes were annotated, 99.70% of which were functionally characterized. An analysis of the presence and arrangement of resistance genes on U. minor, and sister species Ulmus glabra and Ulmus parvifolia, revealed a clustered and syntenic distribution across all of them, with a higher density in U. minor. This genomic resource and its analytical dissection herein introduced represent valuable tools for future in-depth studies on the resistance mechanisms to DED. Additionally, this study completes the phylogenetic context within the order Rosales and provides a robust framework for future research.