DOI: 10.5061/dryad.kwh70rz70
title: A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes

description: 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.
description: Detailed list of files in '.tar.gz' folders:
 Cquinoa_QQ74_v2_pseudomoleculesANDannotations.tar.gz
 --&gt;Cquinoa_QQ74_v2_CDS.fasta (CDS sequences: transcribed
 sequence, devoid of introns, and devoid of UTRs)
 --&gt;Cquinoa_QQ74_v2.fasta (Pseudomolecules and unanchored
 contigs) --&gt;Cquinoa_QQ74_v2.gff3 (Gene
 annotation, including gene, mRNA, CDS, 3' and 5' UTRs)
 --&gt;Cquinoa_QQ74_v2_mRNA.fasta (mRNA sequences: transcribed
 sequence, devoid of introns, but containing UTRs)
 --&gt;Cquinoa_QQ74_v2_prot.fasta (Peptide sequences: CDS
 sequences translated into Amino acid)
 --&gt;Cquinoa_QQ74_v2_REPET_classification.txt (TE
 classification: produced with REPET annotation software)
 --&gt;Cquinoa_QQ74_v2_REPET_consensus.fasta (TE consensus
 sequences: produced with REPET annotation software)
 --&gt;Cquinoa_QQ74_v2_REPET.gff3 (TE annotation: performed
 with REPET software)  
 Csuecicum_v2_pseudomoleculesANDannotations.tar.gz
 --&gt;Csuecicum_v2.fasta (Pseudomolecules and uncanchored
 condigs) --&gt;Csuecicum_v2.gff3 (Gene annotation,
 including gene, mRNA, CDS, 3' and 5' UTRs and tRNA)
 --&gt;Csuecicum_v2_mRNA.fasta (mRNA sequences: transcribed
 sequence, devoid of introns, but containing UTRs)
 --&gt;Csuecicum_v2_prot.fasta (Peptide sequences: CDS
 sequences translated into Amino acid)
 --&gt;Csuecicum_v2_REPET_classification.txt (TE
 classification: produced with REPET annotation software)
 --&gt;Csuecicum_v2_REPET_consensus.fasta (TE consensus
 sequences: produced with REPET annotation software)
 --&gt;Csuecicum_v2_REPET.gff3 (TE annotation: performed with
 REPET software)  
 Cpallidicaule_v2_pseudomoleculesANDannotations.tar.gz
 --&gt;Cpallidicaule_v2.fasta (Pseudomolecules and unanchored
 contigs) --&gt;Cpallidicaule_v2.gff3 (Gene
 annotation, including gene, mRNA, CDS, 3' and 5' UTRs and
 tRNA)  --&gt;Cpallidicaule_v2_mRNA.fasta (mRNA
 sequences: transcribed sequence, devoid of introns, but containing
 UTRs) --&gt;Cpallidicaule_v2_prot.fasta (Peptide
 sequences: CDS sequences translated into Amino acid)
 --&gt;Cpallidicaule_v2_REPET_classification.txt (TE
 classification: produced with REPET annotation software)
 --&gt;Cpallidicaule_v2_REPET_consensus.fasta (TE consensus
 sequences: produced with REPET annotation software)
 --&gt;Cpallidicaule_v2_REPET.gff3 (TE annotation: performed
 with REPET software)  
 Cq_allpseudo_biallelic_minDP5_MaxMissing0.8_MAF0.01.Cq3Bsamples.variantsonly.vcf.tar.gz (SNPs variants among 209 quinoas and wilds called against Cquinoa_QQ74_v2.fasta pseudomolecules: only biallelic variants with minimum read depth 5, maximum missing data 20% and MAF 0.01% were retained)