Terms of access
The genomic data for the bread wheat (Triticum aestivum L.) varieties Alchemy, Brompton, Hereward, Rialto, Soissons, and Xi19 are made available ahead of publication under the principles of the Toronto Agreement (http://www.nature.com/articles/461168a) that grants the generators of these data (The Natural History Museum, NIAB, Earlham Institute, and the John Innes Centre; funded under Biotechnology and Biological Sciences Research Council (BBSRC) grant numbers BB/P010768/1 BB/P010741/1 and BB/P010733/1, the right to publish the first global analyses of the data. This includes descriptions of genome-level and whole chromosome-level analyses.
By accessing and downloading the data, you agree to this principle, and agree to cite the following acknowledgement when disseminating the data: ‘Sequences the bread wheat varieties Alchemy, Brompton, Hereward, Rialto, Soissons, Weebill1 and Xi19 were funded by the BBSRC as part of the project, ‘A wheat pan-genomics platform for enhanced genetic dissection of agronomic traits’, awarded to Matt Clark (Natural History Museum, UK), James Cockram (NIAB, UK), Neil Hall (Earlham Institute, UK) and Mike Bevan (John Innes Centre, UK) under grant numbers BB/P010768/1, BB/P010741/1 and BB/P010733/1. The genomes of Cadenza, Paragon, Claire and Robigus were previously published in 2020 https://www.nature.com/articles/s41586-020-2961-x but have been further assembled into chromosome pseudomolecules as part of the same ‘A wheat pan-genomics platform for enhanced genetic dissection of agronomic traits’ project.
If in doubt about how you can use this data to publish, or for any other questions, please contact matt.clark@nhm.ac.uk or james.cockram@niab.com.
About
Collectively, the eight UK wheat varieties (Alchemy, Brompton, Claire, Hereward, Rialto, Robigus, Soissons and Xi19) represent the founders of the 'NIAB Elite MAGIC' multi-founder advanced generation inter-cross population. The generation of the population is described here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169152. The genome assemblies of six of the NIAB Elite MAGIC founders (Alchemy, Brompton, Hereward, Rialto, Soissons and Xi19), as well as the Mexican variety Weeblill1, were funded by Biotechnology and Biological Sciences (BBSRC) as part of the project, 'A wheat pan-genomics platform for enhanced genetic dissection of agronomic traits', awarded to Matt Clark (Natural History Museum, UK), James Cockram (NIAB, UK), Neil Hall (Earlham Institute, UK) and Mike Bevan (John Innes Centre, UK) under BBSRC grant numbers BB/P010768/1, BB/P010741/1 and BB/P010733/1.
Pseudomolecule genome assemblies for the eight ‘NIAB Elite MAGIC’ founders, plus the varieties Cadenza, Paragon and Weebill1
The scaffold assemblies for the UK wheat cultivars Claire, Robigus (two of the NIAB Elite MAGIC founders), Cadenza and Paragon, as well as the Mexican cultivar Weebill1, were previously published in 2020 https://www.nature.com/articles/s41586-020-2961-x. The remaining six NIAB Elite MAGIC founders (Alchemy, Brompton, Hereward, Rialto, Soissons and Xi19) were assembled to scaffold level, as described in the W2RAP pipeline (http://www.genome.org/cgi/doi/10.1101/gr.217117.116 and https://github.com/bioinfologics/w2rap). Subsequently, for each of the 11 scaffolded assemblies, super-scaffolds and pseudomolecules were made using a guide map by aligning to the chromosome scale pseudomolecule assembly of German winter bread wheat cv. Julius, alongside a contact map derived from the alignment of three-dimensional chromosome conformation capture (Hi-C) sequencing, to order, orientate and curate scaffolds into 21 pseudomolecules (similar to the approach in TRITEX https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1899-5).
To facilitate your analysis, the reference bread wheat genome assembly of cv. Chinese Spring (IWGSC RefSeq v1.0, IWGSC et al. 2018, doi: 10.1126/science.aar7191) has also been included as is.
This BLAST server is hosted by the UK Crop Diversity Bioinformatics HPC Resource which was funded by the BBSRC 18ALERT grant BB/S019669/1.