A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes

Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the
potential to help address global food security concerns. Genomes have been
assembled for three accessions of quinoa; however, all assemblies are
fragmented and do not reflect known chromosome biology. Here, we used in
vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the
Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned
1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds.
The genome was annotated with 54,499 protein-coding genes, 97% of which
were located on the 18 largest scaffolds. We also produced an updated
genome assembly for the B-genome diploid C. suecicum and used it, together
with the A-genome diploid C. pallidicaule, to identify genomic
rearrangements within the quinoa genome, including a large pericentromeric
inversion representing 71.7% of chromosome Cq3B. Repetitive sequences
comprise 65.20%, 48.61%, and 57.91% of the quinoa, C. pallidicaule, and C.
suecicum genomes, respectively. Evidence suggests that the B subgenome is
more dynamic and has expanded more than the A subgenome. These genomic
resources will enable more accurate assessments of genome evolution within
the Amaranthaceae and will facilitate future efforts to identify variation
in genes underlying important agronomic traits in quinoa.