The Genome of Chenopodium quinoa

Chenopodium quinoa (quinoa) is a relative of sugar beet and spinach and is native to the Andean region of South America, where it has adapted to tolerate extreme abiotic stresses, including salinity, drought, heat and frost. Although quinoa has been a staple food source in the region for thousands of years, it has only recently gained international attention due to the high protein content and balanced amino acid composition of its seeds. Short-read sequencing technology previously limited the creation of a gold-standard reference assembly in this allotetraploid (AABB) species. Recent advances in Pacific Biosciences long-read technology have allowed the sequencing of quinoa to approximately 62X coverage, with the aim to understand the genomic features underlying quinoa’s nutritional properties and abiotic stress tolerance. The draft 1.2 Gb assembly is made up of 4971 contigs, with 50 % of the genome assembled in contigs greater than 871 Mb. In addition, 245 Gb (approximately 200X coverage) of BioNano optical map data was generated with the Irys technology to further improve the assembly. The genome annotation was guided by 45 different RNAseq libraries from multiple tissues and treatments, with the goal to generate a gold-standard transcriptome. In addition, the genomes of the related diploid species C. pallidicaule (AA) and C. suecicum (BB) and the related tetraploid species C. hircinum and C. berlandieri have been sequenced to help resolve the evolutionary relationships between quinoa and its relatives. These resources will serve as valuable tools in future genetic improvement of quinoa to increase food security in the face of global climate change and a growing world population.