Genome assemblies of climatically distinct Aegilops mutica reveal extensive structural variation

Bread wheat harbours low genetic diversity due to bottlenecks during speciation, domestication, and selection; wild relatives therefore provide critical reservoir for climate-resilient breeding. Aegilops mutica, one of the few self-incompatible diploids in the Aegilops-Triticum species complex, is a putative parent in the homoploid hybridisation event that formed the D-genome clade and is a proven donor of disease resistance, winter hardiness and grain zinc accumulation. Ae. mutica is globally endangered, with a reference-quality genome available for only a single Central Anatolian accession. Using HiFi sequencing, we generated genome assemblies from two accessions from opposite extremes of the species' range: western Turkiye and Armenia. The four haploid assemblies recovered ~93% complete BUSCOs and comprised ~81% repetitive sequence, predominantly LTR retrotransposons (~55%), closely matching the reference. Comparison against the reference identified 145,871-155,535 structural variants per haplotype, including an 8.4 Mb inversion on chromosome 6T. Between 96,860 and 105,472 structural variants segregated between haplotypes within individuals and classic domestication loci did not overlap with any large structural variants. These assemblies and structural variant catalogue extend genomic resources for Ae. mutica, providing a basis for targeted introgression into wheat and conservation of a species for which populations in the South Caucasus have severely declined.