The homoeolog-resolved assembly of the 40-Gb decaploid Thinopyrum ponticum genome reveals extensive homoeologous exchange and recombination, segmental allopolyploid organization, and allelic variations for wheat improvement.

The decaploid grass Thinopyrum ponticum (Th. ponticum, 2n = 10x = 70) is valuable for improving wheat resilience to biotic and abiotic stressors. However, the high level of ploidy and repetitive nature of its large genome present challenges for genome assembly. We used long-read sequencing and an iterative reassembly strategy to overcome partial haplotype collapse and generate a homoeolog-resolved 41.33-Gb decaploid genome assembly for this grass. Combined comparative genomic, phylogenetic, and k-mer analyses resolved its diploid ancestral origins. Genome-wide recombination-based evidence, corroborated by gametophytic genomic and multiple cytological analyses, further revealed extensive homoeologous exchange consistent with a segmental allopolyploid organization. Annotation of this assembly recovered 577,421 high-confidence genes, the largest gene repertoire reported among Triticeae genomes, including a 22-copy Fhb7 tandem gene cluster distributed across five chromosomes. A wheat-Th. ponticum introgression panel of 348 lines catalogued the beneficial allelic diversity captured in a long-term breeding program, revealing candidate regulators of blue aleurone and identifying an expanded Fhb7 gene cluster as a transferable Fusarium head blight resistance resource. These results provide insights into the structural basis of segmental allopolyploid genome stabilization and offer both a framework and extensive resources to study the basic mechanisms of hybrid introgression and recombination in polyploids.