Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity 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, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies 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.

Brigham Young University Department of Plant and Wildlife Sciences College of Life Sciences Provo UT 84602 USA

Center for Desert Agriculture KAUST Thuwal Saudi Arabia

Fdo LA Esperanza sn Perquenco Chile

INRAE CNRGV French Plant Genomic Resource Center F 31320 Castanet Tolosan France

Institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional Genomics Šlechtitelů 31 CZ 77900 Olomouc Czech Republic

Persephone Software LLC Agoura Hills CA 91301 USA

Plant Science Program Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology Thuwal 23955 6900 Saudi Arabia

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A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium

Genome assembly of a diversity panel of Chenopodium quinoa