KAUST Quinoa genomes

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security in the context of climate change in developing countries. Deep characterization of the diversity of quinoa germplasm at the genetic level is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, about 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies was performed and allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.

藜麦（Chenopodium quinoa）是应对发展中国家气候变化背景下粮食与营养安全未来挑战的关键作物。为支撑全球种植规模扩大过程中藜麦的农艺改良与环境适配，需从遗传层面深度解析藜麦种质资源（germplasm）的多样性。本研究报道了8份藜麦材料的染色体级基因组组装结果，这些材料覆盖了低地与高地藜麦的表型及遗传多样性范围。本次组装结合PacBio HiFi测序读段与Bionano Saphyr光学图谱完成，总组装长度平均为1.28 Gb，平均N50值达71.1 Mb。针对这8个全新藜麦基因组，预测得到的基因模型数量介于43733至48564之间；平均而言，每个藜麦基因组中约66%的序列被归类为重复序列。对8个基因组组装序列进行比对后，成功鉴定出包括倒位、易位与重复在内的多种结构重排事件。这8个全新的藜麦基因组组装结果，可为关联遗传学、比较基因组学及泛基因组（pan-genome）分析提供研究资源，助力挖掘农业重要性状背后的遗传组分与变异。