The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with novel disease-resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata. We establish that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Ae. triuncialis, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.

• The file 'ThatcherLr9_whole_genome_assembly.fasta.gz' contains the DNA sequence of the whole genome assembly of hexaploid bread wheat (Triticum aestivum L. AABBDD, 2n = 6x = 42) cv. ThatcherLr9. The file 'Aegilops_umbellulata_TA1851_whole_genome_assembly.fasta.gz' contains the DNA sequence of the whole genome assembly of diploid Aegilops umbellulata (UU, 2n = 2x = 14) accession TA1851. Data was produced using PacBio HiFi sequencing and assembled with Hifiasm.
• The files 'ThatcherLr9_IsoSeq_cluster_hq.fasta.gz' and 'TA5605_IsoSeq_cluster_hq.fasta.gz' contain high-quality transcript isoforms from Puccinia triticina infected leaf samples of ThatcherLr9 and TA5605, respectively. Data was produced using PacBio long-read isoform sequencing (Iso-Seq) and processed following the IsoSeq pipeline (v.3.; https://github.com/PacificBiosciences/IsoSeq).
• The Lr9 CDS and genomic sequences are present in FASTA format.