DOI: 10.5061/dryad.vmcvdnd0d
title: Population genomics of the wild wheat Aegilops tauschii (Open wild wheat consortium phase II)

description: Wild wheat relatives of bread wheat represent genetic diversity that can
 be used for wheat crop improvement. Here, we establish and analyse genomic
 resources for Tausch’s goatgrass, Aegilops tauschii, the donor of the
 bread wheat D genome. We determined 493 genetically non-redundant
 accessions from a diversity panel of over 900 sequenced accessions. We
 generated high-quality assemblies for 46 accessions, including annotated
 chromosome-scale assemblies for one accession from each of the three
 lineages of Ae. tauschii to serve a reference assemblies to anchor the
 genomic resources. This dataset was generated under the aegis of the Open
 Wild Wheat Consortium (www.openwildwheat.org). We also resequenced and
 analysed 60 wheat landraces and generated a chromosome-scale genome
 assembly for one of these to study the genetic composition and history of
 the bread wheat D genome. We determined the complexity and origin of the D
 genome across 17 hexaploid wheat lines by dividing the wheat genomes into
 50-kb windows and assigned each window to an Ae. tauschii subpopulation
 based on identity-by-state. This dataset provides: Pseudo-chromosome level
 genome assemblies, Hi-C contact maps and genome annotations for the Ae.
 tauschii lineage-reference accessions TA10171 (L1), TA1675 (L2) and TA2576
 (L3), Contig-level and lineage reference-scaffolded assemblies for 43 Ae.
 tauschii accessions sequenced with PacBIO CCS Pseudo-chromosome level
 genome assembly, Omni-C contact map and genome annotation
 for bread wheat landrace accession CWI 86942, Variant call (SNP)
 vcf file for the Ae. tauschii diversity panel. SNP were called against the
 TA1675 (L2) reference assembly, Phylogenetic newick tree file for the
 non-redundant Ae. tauschii accessions, Structural variants (SV)
 vcf files for Ae. tauschii accessions sequenced with PacBIO CCS. SV were
 called against the TA1675 (L2) reference assembly, IBSpy variations across
 17 hexaploid wheat genomes using Ae. tauschii k-mer sets
description: The full methods are available in the related publication.
description: # Population genomics of the wild wheat Aegilops tauschii (Open Wild Wheat
 Consortium Phase II)
 [https://doi.org/10.5061/dryad.vmcvdnd0d](https://doi.org/10.5061/dryad.vmcvdnd0d) ## Description of the data and file structure Wild wheat relatives of bread wheat represent genetic diversity that can be used for wheat crop improvement. Here, we establish and analyse genomic resources for Tausch’s goatgrass, *Aegilops tauschii*, the donor of the bread wheat D genome. We determined 493 genetically non-redundant accessions from a diversity panel of over 900 sequenced accessions. We generated high-quality assemblies for 46 accessions, including annotated chromosome-scale assemblies for one accession from each of the three lineages of Ae. tauschii to serve a reference assemblies to anchor the genomic resources. This dataset was generated under the aegis of the Open Wild Wheat Consortium ([www.openwildwheat.org](https://www.openwildwheat.org)). We also resequenced and analysed 60 wheat landraces and generated a chromosome-scale genome assembly for one of these to study the genetic composition and history of the bread wheat D genome. We determined the complexity and origin of the D genome across 17 hexaploid wheat lines by dividing the wheat genomes into 50-kb windows and assigned each window to an *Ae. tauschii* subpopulation based on identity-by-state. This dataset provides: Pseudo-chromosome-level genome assemblies (.fasta.gz), Hi-C contact maps (.assembly.gz and .hic.gz) and gene and repeat annotations (.gff3.gz), and predicted cds and protein sequences (.cds and .aa) for the *Ae. tauschii* lineage reference accessions TA10171 (Lineage 1), TA1675 (Lineage 2) and TA2576 (Lineage 3). The corresponding files are as follow: * AetTA10171_L1.Ref.genome.fasta.gz * AetTA1675_L2.Ref.genome.fasta.gz * AetTA2576_L3.Ref.genome.fasta.gz * AetTA10171_assembly.final.assembly.gz * AetTA10171_assembly.final.hic.gz * AetTA1675_assembly.final.assembly.gz * AetTA1675_assembly.final.hic.gz * AetTA2576_assembly.final.assembly.gz * AetTA2576_assembly.final.hic.gz * AetTA10171_v1.gff3.gz * AetTA1675_v1.gff3.gz * AetTA2576_v1.gff3.gz * AetTA10171_v1.cds * AetTA1675_v1.cds * AetTA2576_v1.cds * AetTA10171_v1.aa * AetTA1675_v1.aa * AetTA2576_v1.aa * AetTA10171_repeats_v1.gff.gz * AetTA10171_repeats_v1.tbl.gz * AetTA1675_repeats_v1.gff.gz * AetTA1675_repeats_v1.tbl.gz * AetTA2576_repeats_v1.gff.gz * AetTA2576_repeats_v1.tbl.gz Primary contig-level assemblies (.hifiasm.bp.p_ctg.fa.gz)  for 43 *Ae. tauschii* accessions sequenced with PacBIO CCS (HiFi). The reference-based scaffolded assemblies (.scaffold.fsa.gz) were scaffolded using RagTag and the corresponding Lineage 1 (TA10171ref) or Lineage 2 (TA1675ref) reference assembly. Information on the RagTag ordering and orientations of the contigs per accession in AGP format is included in the Excel file (.xlsx). The scaffolded genomes were visually inspected through dotplots by whole genome alignment to their corresponding lineage reference (.docx). The corresponding files are: * TOWWC0243.hifiasm.bp.p_ctg.fa.gz * TOWWC0242.hifiasm.bp.p_ctg.fa.gz * TOWWC0240.hifiasm.bp.p_ctg.fa.gz * TOWWC0236.hifiasm.bp.p_ctg.fa.gz * TOWWC0212.hifiasm.bp.p_ctg.fa.gz * TOWWC0202.hifiasm.bp.p_ctg.fa.gz * TOWWC0191.hifiasm.bp.p_ctg.fa.gz * TOWWC0187.hifiasm.bp.p_ctg.fa.gz * TOWWC0182.hifiasm.bp.p_ctg.fa.gz * TOWWC0178.hifiasm.bp.p_ctg.fa.gz * TOWWC0169.hifiasm.bp.p_ctg.fa.gz * TOWWC0167.hifiasm.bp.p_ctg.fa.gz * TOWWC0163.hifiasm.bp.p_ctg.fa.gz * TOWWC0152.hifiasm.bp.p_ctg.fa.gz * TOWWC0144.hifiasm.bp.p_ctg.fa.gz * TOWWC0142.hifiasm.bp.p_ctg.fa.gz * TOWWC0137.hifiasm.bp.p_ctg.fa.gz * TOWWC0123.hifiasm.bp.p_ctg.fa.gz * TOWWC0131.hifiasm.bp.p_ctg.fa.gz * TOWWC0112.hifiasm.bp.p_ctg.fa.gz * TOWWC0107.hifiasm.bp.p_ctg.fa.gz * TOWWC0088.hifiasm.bp.p_ctg.fa.gz * TOWWC0106.hifiasm.bp.p_ctg.fa.gz * TOWWC0083.hifiasm.bp.p_ctg.fa.gz * TOWWC0073.hifiasm.bp.p_ctg.fa.gz * TOWWC0050.hifiasm.bp.p_ctg.fa.gz * TOWWC0054.hifiasm.bp.p_ctg.fa.gz * TOWWC0047.hifiasm.bp.p_ctg.fa.gz * TOWWC0023.hifiasm.bp.p_ctg.fa.gz * TOWWC0002.hifiasm.bp.p_ctg.fa.gz - TOWWC0111.hifiasm.bp.p_ctg.fa.gz - TOWWC0162.hifiasm.bp.p_ctg.fa.gz - TOWWC0190.hifiasm.bp.p_ctg.fa.gz * Tajik1040.hifiasm.bp.p_ctg.fa.gz * TA10097.hifiasm.bp.p_ctg.fa.gz * PI690713.hifiasm.bp.p_ctg.fa.gz * TA1618.hifiasm.bp.p_ctg.fa.gz * RL5271.hifiasm.bp.p_ctg.fa.gz * P999511.hifiasm.bp.p_ctg.fa.gz * AL878.hifiasm.bp.p_ctg.fa.gz * TOWWC0078.hifiasm.bp.p_ctg.fa.gz * TOWWC0031.hifiasm.bp.p_ctg.fa.gz - TOWWC243.TA10171ref.scaffold.fsa.gz * TOWWC242.TA10171ref.scaffold.fsa.gz * TOWWC240.TA10171ref.scaffold.fsa.gz * TOWWC236.TA10171ref.scaffold.fsa.gz * TOWWC212.TA10171ref.scaffold.fsa.gz * TOWWC202.TA10171ref.scaffold.fsa.gz * TOWWC191.TA1675ref.scaffold.fsa.gz * TOWWC190.TA1675ref.scaffold.fsa.gz * TOWWC187.TA1675ref.scaffold.fsa.gz * TOWWC182.TA1675ref.scaffold.fsa.gz * TOWWC178.TA1675ref.scaffold.fsa.gz * TOWWC169.TA1675ref.scaffold.fsa.gz * TOWWC167.TA1675ref.scaffold.fsa.gz * TOWWC163.TA1675ref.scaffold.fsa.gz * TOWWC162.TA1675ref.scaffold.fsa.gz * TOWWC152.TA1675ref.scaffold.fsa.gz * TOWWC144.TA1675ref.scaffold.fsa.gz * TOWWC142.TA1675ref.scaffold.fsa.gz * TOWWC137.TA1675ref.scaffold.fsa.gz * TOWWC131.TA1675ref.scaffold.fsa.gz * TOWWC123.TA1675ref.scaffold.fsa.gz * TOWWC112.TA1675ref.scaffold.fsa.gz * TOWWC111.TA1675ref.scaffold.fsa.gz * TOWWC107.TA1675ref.scaffold.fsa.gz * TOWWC106.TA1675ref.scaffold.fsa.gz * TOWWC088.TA1675ref.scaffold.fsa.gz * TOWWC083.TA1675ref.scaffold.fsa.gz * TOWWC073.TA1675ref.scaffold.fsa.gz * TOWWC078.TA1675ref.scaffold.fsa.gz * TOWWC054.TA10171ref.scaffold.fsa.gz * TOWWC050.TA1675ref.scaffold.fsa.gz * TOWWC047.TA1675ref.scaffold.fsa.gz * TOWWC031.TA1675ref.scaffold.fsa.gz * TOWWC023.TA1675ref.scaffold.fsa.gz * TOWWC002.TA1675ref.scaffold.fsa.gz * Tajik1040.TA10171ref.scaffold.fsa.gz * TA10097.TA10171ref.scaffold.fsa.gz * TA1618.TA1675ref.scaffold.fsa.gz * RL5271.TA1675ref.scaffold.fsa.gz * PI690713.TA1675ref.scaffold.fsa.gz * P999511.TA10171ref.scaffold.fsa.gz * ENT336.TA1675ref.scaffold.fsa.gz * AL878.TA1675ref.scaffold.fsa.gz * agp_files_from_ragtag_scaffold.xlsx * dotplots_ragtag_scaffold.docx Pseudo-chromosome level genome assembly (.fasta.gz), pseudomolecules and Omni-C contact map (assembly.gz and hic.gz) and genome annotation (.gff3.gz) for bread wheat landrace accession CWI 86942. The corresponding files are: * TaesCWI86942_genome.fasta.gz - TaesCWI86942_assembly.final.assembly.gz * TaesCWI86942_assembly.omnic.hic.gz * TaesCWI86942_v1.gff3.gz Variant calling (SNP) file (.vcf.gz) for the *Ae. tauschii* diversity panel. SNPs were called against the TA1675 (L2) reference assembly. The corresponding file is: * SNP_call_Aet.vcf.tar.gz Phylogenetic newick tree file (.nwk) for 493 non-redundant *Ae. tauschii* accessions. The corresponding file is: * upgma_Aet_NonRed.nwk Structural variants (SV) files (.vcf.gz) for *Ae. tauschii* accessions sequenced with PacBIO CCS (HiFi). SV were called from the HiFi reads aligned to the TA1675 (L2) reference genome assembly. The corresponding files are: * SV_TA1675ref.AL878.vcf.gz * SV_TA1675ref.PI690713.vcf.gz * SV_TA1675ref.ENT336.vcf.gz * SV_TA1675ref.TA1618.vcf.gz * SV_TA1675ref.RL5271.vcf.gz * SV_TA1675ref.TOWWC002.vcf.gz * SV_TA1675ref.TOWWC023.vcf.gz * SV_TA1675ref.TOWWC047.vcf.gz * SV_TA1675ref.TOWWC050.vcf.gz * SV_TA1675ref.TOWWC073.vcf.gz * SV_TA1675ref.TOWWC088.vcf.gz * SV_TA1675ref.TOWWC083.vcf.gz * SV_TA1675ref.TOWWC107.vcf.gz * SV_TA1675ref.TOWWC106.vcf.gz * SV_TA1675ref.TOWWC111.vcf.gz * SV_TA1675ref.TOWWC112.vcf.gz * SV_TA1675ref.TOWWC123.vcf.gz * SV_TA1675ref.TOWWC131.vcf.gz * SV_TA1675ref.TOWWC137.vcf.gz * SV_TA1675ref.TOWWC142.vcf.gz * SV_TA1675ref.TOWWC144.vcf.gz * SV_TA1675ref.TOWWC152.vcf.gz * SV_TA1675ref.TOWWC162.vcf.gz * SV_TA1675ref.TOWWC163.vcf.gz * SV_TA1675ref.TOWWC169.vcf.gz - SV_TA1675ref.TOWWC167.vcf.gz * SV_TA1675ref.TOWWC182.vcf.gz * SV_TA1675ref.TOWWC187.vcf.gz * SV_TA1675ref.TOWWC178.vcf.gz * SV_TA1675ref.TOWWC190.vcf.gz * SV_TA1675ref.TOWWC191.vcf.gz * SV_TA1675ref.TA2576.vcf.gz * SV_TA1675ref.Tajik1040.vcf.gz * SV_TA1675ref.TOWWC243.vcf.gz * SV_TA1675ref.TOWWC242.vcf.gz * SV_TA1675ref.TOWWC240.vcf.gz * SV_TA1675ref.TOWWC236.vcf.gz * SV_TA1675ref.TOWWC212.vcf.gz * SV_TA1675ref.TOWWC202.vcf.gz * SV_TA1675ref.TOWWC054.vcf.gz * SV_TA1675ref.TA10171.vcf.gz * SV_TA1675ref.TA10097.vcf.gz * SV_TA1675ref.P999511.vcf.gz IBSpy variations across 17 hexaploid wheat genomes using *Ae. tauschii* *k*-mer sets (.csv and .tsv.gz). The file names begin with the wheat accession ID. The corresponding files are: * CWI86942_50kb_windows_predictions.csv * CWI86942_aetauschii_combined_queries_50000w.tsv.gz * PI190962_50kb_windows_predictions.csv * PI190962_aetauschii_combined_queries_50000w.tsv.gz * aikang58_50kb_windows_predictions.csv * aikang58_aetauschii_combined_queries_50000w.tsv.gz * arinalrfor_50kb_windows_predictions.csv * arinalrfor_aetauschii_combined_queries_50000w.tsv.gz * attraktion_50kb_windows_predictions.csv * attraktion_aetauschii_combined_queries_50000w.tsv.gz * cdclandmark_50kb_windows_predictions.csv * cdclandmark_aetauschii_combined_queries_50000w.tsv.gz * chinese_spring_50kb_windows_predictions.csv * chinese_spring_aetauschii_combined_queries_50000w.tsv.gz * fielder_50kb_windows_predictions.csv * fielder_aetauschii_combined_queries_50000w.tsv.gz * jagger_50kb_windows_predictions.csv * jagger_aetauschii_combined_queries_50000w.tsv.gz * julius_50kb_windows_predictions.csv * julius_aetauschii_combined_queries_50000w.tsv.gz * kariega_50kb_windows_predictions.csv * kariega_aetauschii_combined_queries_50000w.tsv.gz * longreachlancer_50kb_windows_predictions.csv * longreachlancer_aetauschii_combined_queries_50000w.tsv.gz * mace_50kb_windows_predictions.csv * mace_aetauschii_combined_queries_50000w.tsv.gz * norin61_50kb_windows_predictions.csv * norin61_aetauschii_combined_queries_50000w.tsv.gz * stanley_50kb_windows_predictions.csv * stanley_aetauschii_combined_queries_50000w.tsv.gz * symattis_50kb_windows_predictions.csv * symattis_aetauschii_combined_queries_50000w.tsv.gz * zang1817_50kb_windows_predictions.csv * zang1817_aetauschii_combined_queries_50000w.tsv.gz