Data & tools

Browse the UWA wheat assemblies online, download them, or search them with BLAST. Please cite the paper listed with each resource if you use it.

Genome browsers

Wheat pangenome v1.0

• Wheat pangenome GBrowse (UWA_1.0)

Cite: Montenegro JD et al. (2017) The pangenome of hexaploid bread wheat. The Plant Journal 90: 1007–1013. doi:10.1111/tpj.13515

Chromosome group 7, version 2.0

• Wheat 7A · Wheat 7B · Wheat 7D

Described in: Berkman PJ et al. (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal 11: 564–571. doi:10.1111/pbi.12044

Chromosome group 7, early version 0.1 (chromosome arms)

• 7AS · 7AL · 7BS · 7BL · 7DS · 7DL

Described in: Berkman PJ et al. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal 9: 768–775. doi:10.1111/j.1467-7652.2010.00587.x · Berkman PJ et al. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics 124: 423–432. doi:10.1007/s00122-011-1717-2

Wheat Panache: pangenome graph of 16 bread wheat genomes

• Wheat Panache: browse gene presence/absence variation across 16 bread wheat genome assemblies, chromosome by chromosome.

Cite: Bayer PE et al. (2022) Wheat Panache: a pangenome graph database representing presence–absence variation across sixteen bread wheat genomes. The Plant Genome 15: e20221. doi:10.1002/tpg2.20221

Watkins wheat pangenome

• Watkins Explorer: gene presence/absence across the Watkins landrace collection and modern cultivars, by ancestral group, country and growth habit; BLAST, gene pages, downloads, trial phenotypes and a JSON API.

Downloads

Wheat pangenome v1.0: assemblies and SNPs by chromosome

Checksums: assembly md5 file · SNP md5 file. Check a download with md5sum -c.

Wheat pangenome v1.0: genes, proteins and presence/absence

Group 7 v2.0 SNPs: Lai K et al. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13: 97–104. doi:10.1111/pbi.12240. SNPs were called with SGSautoSNP: Lorenc MT et al. (2012) Biology 1: 370–382. doi:10.3390/biology1020370

Raw sequence reads and any data not listed here are available on request.

Analysis tools

• askWheat: one search across Ensembl Plants, the Watkins pangenome and CropSNPdb, plus a free MCP server so AI assistants such as Claude can answer wheat questions with cited sources (how to connect). Part of the International Wheat Information System (WheatIS).
• BLAST portal: search the wheat assemblies; results link straight to the matching location in GBrowse.
• Wheat autoSNPdb: SNPs identified in wheat expressed sequence tags (ESTs). Cite: Duran C et al. (2009) Nucleic Acids Research 37: D951–D953. doi:10.1093/nar/gkn650
• CropSNPdb: search and download wheat SNP array genotypes: the 40K Australian Grains Genebank set (about 28,900 lines) and the 90K array for 309 lines (data from T3 Wheat), plus Brassica 60K array data. Also available through a JSON API. Cite: Scheben A et al. (2019) CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. The Plant Journal 98: 142–152. doi:10.1111/tpj.14194