Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
Sci Data. 2023 Oct 25;10(1):739. doi: 10.1038/s41597-023-02658-2.
Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.
野生小麦近缘种在植物育种中得到了广泛的研究，以增加作为最重要粮食作物之一的栽培小麦的遗传多样性。节节麦是一种含有 U 基因组的二倍体草种，是小麦改良的遗传资源库。在这项研究中，我们报告了基于修正后的 PacBio HiFi reads 和染色体构象捕获技术构建的节节麦 TA1851 品系的染色体水平参考基因组组装。总组装大小为 42.5 Mb，contig N50 为 17.7 Mb。总共预测了 36268 个基因模型。我们使用标准和修正的 HiFi reads 对两种最广泛使用的组装器 hifiasm 和 LJA 的性能进行了基准测试，结果表明修正后的输入 reads 具有积极的效果。比较基因组分析证实，与栽培小麦相比，节节麦的染色体发生了大量重排。总之，节节麦的基因组组装为三芒草属的比较基因组学研究和农业上重要基因的发现提供了资源。
