The genome of Chenopodium pallidicaule : An emerging Andean super grain.

Premise Canahua is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Canahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. Methods The reference assembly was developed using a combination of short- and long-read sequencing techniques, including multiple rounds of Hi-C-based proximity-guided assembly. Results The final assembly of the similar to 363-Mbp genome consists of 4633 scaffolds, with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common repeat identified as long terminal repeat retrotransposons. MAKER annotation of the final assembly yielded 22,832 putative gene models. Discussion When compared with quinoa, strong patterns of synteny support the hypothesis that canahua is a close A-genome diploid relative, and thus potentially a simplified model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of canahua accessions suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.