Triticum aestivum cultivars

UK Wheat Lines

Five wheat lines chosen for their importance in breeding and research in the United Kingdom have been sequenced and displayed in Ensembl as part of our contribution to the Designing Future Wheat project. This includes Claire, Cadenza, Paragon, Robigus and Weebill.

These scaffold-level assemblies were sequenced at the Earlham Institute as part of the wheat pan genome. Sequencing was performed on an Illumina HiSeq 2500 instrument with a 2x250 bp read metric targeting 45x raw coverage of the amplification-free library and 25x coverage of a combination of mate-pair libraries with inserts sizes >7 Kbp. Between 44 and 51x paired-end genome coverage was generated per line. Contigging was performed using the w2rap-contigger using k=200. Two mate-pair libraries were produced for each line except Weebill, where five libraries were used. Mate-pairs were processed, filtered and used to scaffold contigs as described in the w2rap pipeline. Scaffolds less than 500bp were removed from the final assemblies. The K-mer Analysis Toolkit was used to validate scaffolds by generating a kmer histogram from the matrix of kmers shared between the paired-end reads and the scaffolds.

Paragon genome is updated from scaffold to chromosome assembly. The genome was sequenced and assembled at Earlham Institute using PacBio HiFi reads (33x coverage) and Oxford Nanopore ultra-long reads (17x coverage), then scaffolded using Omni-C reads to generate a chromosome-scale assembly. This resource was produced as part of the UK Biotechnology and Biological Sciences Research Council's Delivering Sustainable Wheat project.

IWGSC RefSeq v2.1

The genome assembly of the reference Triticum aestivum cv. Chinese Spring (IWGSC RefSeq v1.0) was revised using whole genome optical maps and contigs assembled from whole-genome-shotgun (WGS) PacBio SMRT reads. PacBio contigs were used for gap closing. Pseudomolecules of the Chinese Spring 21 chromosomes were re-constructed to develop a new reference sequence, IWGSC RefSeq v2.1. The revisions involved approximately 10% sequence length of the IWGSC RefSeq v1.0.

• Walkowiak, S., Gao, L., Monat, C. et al. Multiple wheat genomes reveal global variation in modern breeding. Nature (2020). https://doi.org/10.1038/s41586-020-2961-x
• Tingting Zhu, Le Wang, Hélène Rimbert et al. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. The Plant Journal (2021). https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.15289