Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high-quality near telomere-to-telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present-day U-genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub-populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat.

中文翻译：

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Aegilops umbellulata 的基因组为 U 基因组中独特的结构变异和遗传多样性提供了新的见解，用于小麦改良


Aegilops umbellulata 是小麦改良的新型生物和非生物胁迫耐受性的重要储存库。然而，该物种的染色体重排和进化轨迹仍有待阐明。在这里，我们通过生成 PI 554389 的高质量近端粒到端粒基因组组装并重新测序代表不同地理和表型变异的另外 20 个 Ae. umbellulata 基因组，对 Ae. umbellulata 基因组进行了全面研究。我们的分析揭示了复杂的染色体重排，最突出的是 4U 和 6U 染色体，描绘了 Ae. umbellulata 与小麦及其亲缘种的不同进化轨迹。此外，我们的数据纠正了过去染色体 4U 和 6U 的错误命名，并突出了导致当今 U 基因组的多个主要进化事件。对不同的 Ae. umbellulata 种质的重新测序揭示了该物种内的高度遗传多样性，分为三个不同的进化亚群，并得到了对五种主要小麦病害的几个种族/病型的抗性的广泛表型变异的支持。疾病评估表明，重测序系中存在几种新的耐药基因，用于未来的研究。重测序还导致鉴定出 Lr9 的 6 种新单倍型，Lr9 是从 Ae. umbellulata 克隆的第一个抗性基因。本研究中提出的广泛的基因组和表型资源将加快 Ae. umbellulata 的未来遗传探索，促进旨在提高小麦弹性和生产力的努力。