Genome assemblies of climatically distinct Aegilops mutica reveal extensive structural variation

Abstract

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 Türkiye 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. Plain language summary Bread wheat has limited genetic diversity due to selection, making it vulnerable to climate change and disease. Crop wild relatives contain useful variation that could be used to breed more resilient crops. Aegilops mutica is an endangered wild grass related to wheat that has been used before for disease resistance and other traits. We sequenced two plants originally collected from opposite ends of its range – western Türkiye and Armenia. We found over 100,000 large-scale differences per plant between our new genomes and the reference genome, including one rearrangement over 8 million DNA bases long. Even within one plant, the two copies of its genome contained many differences, as Aegilops mutica must always cross-pollinate to reproduce. These findings increase our knowledge of this endangered species, providing wheat breeders with additional resources and conservationists with a baseline of its genetic diversity across its range.