DOI: 10.5061/dryad.zkh1893jj
title: Data from: Genome assembly of a diversity panel of Chenopodium quinoa

description: Quinoa is an important crop for the future challenges of food and nutrient
 security in the context of climate changes in developing countries. Deep
 characterization of the genetic diversity of quinoa germplasm at both
 genetic and genomic levels is needed to support quinoa agronomical
 improvement and adaptation following its worldwide cultivation expansion.
 In this study, we report the construction of chromosome-scale genome
 assemblies of eight C. quinoa accessions covering the spread of phenotypic
 and genetic diversity of both Lowland and Highland quinoas. The assemblies
 were produced from a combination of PacBio HiFi reads and Bionano Saphyr
 optical maps, with total assembly sizes averaging 1.28 Gb with an average
 N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for
 the eight new quinoa genomes, and on average, about 66% of each quinoa
 genome was classified as repetitive sequences. Alignment between the eight
 genome assemblies was performed and allowed the identification of
 structural rearrangements including inversion, translocation, and
 duplication. In summary, these eight novel C. quinoa genome
 assemblies provide a resource for association genetics, comparative
 genomics, and pan-genome analyses for the discovery of genetic components
 and variations underlying agriculturally important traits.
description: Here we present the genome assembly and annotation of a panel of
 eight quinoa accessions of diverse geographical origins selected to
 represent the diversity of quinoa phenotypes and to support the genetic
 improvement and adaptation of quinoa to warm and arid environments. All
 eight genomes are high-quality chromosome-scale reference sequences
 assembled from over 30x genome coverage of PacBio HiFi long-reads further
 validated by Bionano Saphyr optical maps. We further provide a map of
 structural rearrangements (inversion, duplication, and translocation)
 between the eight genomes. Altogether, these datasets represent important
 resources for the investigation of the genetic components underlying
 important agronomical traits for quinoa improvement to meet the challenges
 of domestication and adaptation to its novel environments of
 cultivation.
description: # Genome assembly of a diversity panel of Chenopodium quinoa
 [https://doi.org/10.5061/dryad.zkh1893jj](https://doi.org/10.5061/dryad.zkh1893jj) ## Brief summary Here we present the genome assembly and annotation of a panel of eight quinoa accessions of diverse geographical origins. They were selected to represent the diversity of phenotypes (growth habit, panicle architecture, leaf shape, stem and seed colors) and for performing well in hot, dry and short-days environments. The eight quinoa accessions include three Lowland (REGALONA acc. KAUST-09303 and JAVI acc. KAUST-09307 from Chile; D-12282 acc. KAUST-09300 from Argentina) and five Highland genotypes (CHEN-199 acc. KAUST-09372 and PI-614919 acc. KAUST-09363 from Bolivia; 03-21-072RM acc. KAUST-09370, D-10126 acc. KAUST-09362 and CHEN-90 acc. KAUST-09367 from Peru). All eight genomes are high-quality chromosome-scale reference sequences assembled from over 30x genome coverage of PacBio HiFi long-reads further validated by Bionano Saphyr optical maps. The annotation of the repeat elements across the 8 quinoa genomes was performed using panEDTA with the REPET curated library provided for QQ74-V2 as input. The gene models were predicted using a combination of lifting and genome-guided approach supported by IsoSeq dataset for Regalona and 0321072RM accessions, and a lifted approach from a merged and curated annotation between Regalona, 0321072RM and QQ74-V2 for the other 6 accessions. ## Description of the data and file structure Detailed list of files in '.tar.gz' folders: ### Final\_Regalona.tar.gz \--&gt;Regalona.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;Regalona_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;Regalona_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;Regalona_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;Regalona_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_PI614919.tar.gz \--&gt;PI614919.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;PI614919_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;PI614919_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;PI614919_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;PI614919_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_Javi.tar.gz \--&gt;Javi.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;Javi_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;Javi_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;Javi_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;Javi_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_D12282.tar.gz \--&gt;D12282.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;D12282_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;D12282_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;D12282_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;D12282_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_D10126.tar.gz \--&gt;D10126.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;D10126_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;D10126_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;D10126_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;D10126_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_CHEN199.tar.gz \--&gt;CHEN199.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;CHEN199_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;CHEN199_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;CHEN199_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;CHEN199_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_CHEN90.tar.gz \--&gt;CHEN90.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;CHEN90_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;CHEN90_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;CHEN90_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;CHEN90_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Final\_0321072RM.tar.gz \--&gt;0321072RM.fasta.mod.EDTA.TEanno.gff3 (Repeat annotation performed with EDTA using the REPET curated library from QQ74-V2 reference genome) \--&gt;0321072RM_v1.gff3 (Gene annotation: gene, mRNA, exon and CDA coordinates) \--&gt;0321072RM_v1.fasta (Genome assembly: pseudomolecules and unanchored (UA) contigs) \--&gt;0321072RM_v1-prot.fasta (Peptide sequences: CDS sequences translated into Amino acid) \--&gt;0321072RM_v1-cds.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs) ### Additional files: \--&gt;Quinoa_panEDTA.TElib.fa.tar.gz (Consolidated repeat elements library produced by panEDTA from all 8 quinoa accessions + QQ74-V2) \--&gt;tidk-plots.zip (Output plots produced by tidk (v.0.2.31) (Brown et al. 2023) to detect pics of telomeric repeats in the assemblies)