Reference sequence of Aegilops umbellulata TA1851

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.

野生小麦近缘物种已被应用于植物育种工作，以提升作为全球最重要粮食作物之一的面包小麦的遗传多样性。伞穗山羊草（Aegilops umbellulata）是一种携带U基因组的二倍体草本植物，是小麦遗传改良的重要遗传资源库。本研究中，我们基于校正后的PacBio HiFi读段与染色体构象捕获数据，完成了伞穗山羊草TA1851品系的染色体级参考基因组组装。该组装的总长度为4.25 Gb，重叠群N50达17.7 Mb，共预测得到36268个基因模型。我们采用标准与校正后的HiFi读段，对两款应用最广泛的基因组组装工具hifiasm与LJA的性能开展了基准测试，结果证实校正后的输入读段可对组装效果产生正向提升作用。比较基因组分析证实，相较于面包小麦，伞穗山羊草存在大量染色体结构重排事件。综上，本次构建的伞穗山羊草参考基因组组装，可为小麦族（Triticeae）的比较基因组学研究以及农艺重要基因的发掘提供核心资源。