Population genomics of the wild wheat Aegilops tauschii (Open wild wheat consortium phase II)

<p>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, <em>Aegilops tauschii</em>, 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 (<a href="https://www.openwildwheat.org">www.openwildwheat.org</a>). 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.</p> <p>This dataset provides:</p> <ol> <li>Pseudo-chromosome level genome assemblies, Hi-C contact maps and genome annotations for the <em>Ae. tauschii</em> lineage-reference accessions TA10171 (L1), TA1675 (L2) and TA2576 (L3),</li> <li>Contig-level and lineage reference-scaffolded assemblies for 43 Ae. tauschii accessions sequenced with PacBIO CCS</li> <li>Pseudo-chromosome level genome assembly, Omni-C contact map and genome annotation for bread wheat landrace accession CWI 86942,</li> <li>Variant call (SNP) vcf file for the <em>Ae. tauschii </em>diversity panel. SNP were called against the TA1675 (L2) reference assembly,</li> <li>Phylogenetic newick tree file for the non-redundant <em>Ae. tauschii</em> accessions,</li> <li>Structural variants (SV) vcf files for Ae. tauschii accessions sequenced with PacBIO CCS. SV were called against the TA1675 (L2) reference assembly,</li> <li>IBSpy variations across 17 hexaploid wheat genomes using Ae. tauschii k-mer sets </li> </ol>