A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Communications Biology Year : 2023

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

Elodie Rey
Peter Maughan
  • Function : Author
Florian Maumus
Daniel Lewis
Leanne Wilson
  • Function : Author
Juliana Fuller
  • Function : Author
Sandra Schmöckel
  • Function : Author
Eric Jellen
Mark Tester
David Jarvis

Abstract

Abstract Quinoa ( Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use 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 65.2%, 48.6%, and 57.9% 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.

Dates and versions

hal-04344166 , version 1 (14-12-2023)

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Elodie Rey, Peter Maughan, Florian Maumus, Daniel Lewis, Leanne Wilson, et al.. A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes. Communications Biology, 2023, 6 (1), pp.1263. ⟨10.1038/s42003-023-05613-4⟩. ⟨hal-04344166⟩
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