Genome assembly of a diversity panel of Chenopodium quinoa

Quinoa is an important crop for the future challenges of food and nutrient security in the context of climate changes in developing countries. Deep characterization of the genetic diversity of quinoa germplasm at both genetic and genomic levels is needed to support quinoa agronomical improvement and adaptation following its worldwide cultivation expansion. In this study, we report the construction of chromosome-scale genome assemblies of eight C. quinoa accessions covering the spread 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 an average 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 inversion, translocation, and duplication. In summary, these eight novel C. 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.

Methods
Here we present the genome assembly and annotation of a panel of eight quinoa accessions of diverse geographical origins selected to represent the diversity of quinoa phenotypes and to support the genetic improvement and adaptation of quinoa to warm and arid environments. All eight genomes are high-quality chromosome-scale reference sequences assembled from over 30x genome coverage of PacBio HiFi long-reads further validated by Bionano Saphyr optical maps. We further provide a map of structural rearrangements (inversion, duplication, and translocation) between the eight genomes. Altogether, these datasets represent important resources for the investigation of the genetic components underlying important agronomical traits for quinoa improvement to meet the challenges of domestication and adaptation to its novel environments of cultivation.