Wheat assemblies

Ensembl Plants hosts the RefSeq v1.0 assembly from the IWGSC, including:

• The IWGSC RefSeq v1.1 gene annotation, with links to wheat expression browser and KnetMiner
• 19 wheat cultivars from the 10+ genome project and other sources including comparative analysis across the different lines
• ~90 million variants from the Watkins Landrace Wheat Collection
• Variants were loaded from the Triticum aestivum Next GenerationTaNG array derived from 204 elite wheat lines and 111 wheat landraces from the Watkins 'Core Collection'
• Axiom 35K, 820K SNP arrays from CerealsDB, including QTL links in selected cases and Linkage Disequilibrium display - see QTL example here. 820K variants have been lifted over to the chromosomal level 10+ wheat cultivars
• EMS-induced mutations from sequenced TILLING populations of Cadenza (coding regions) and Kronos (coding regions and promoters)
• Inter-Homeologous Variants (IHVs) between the A, B and D genome components
• Chromosome specific KASP markers from the Nottingham BBSRC Wheat Research Centre
• Whole genome alignments to rice, brachypodium and barley
• Polyploid view enabled, allowing users to view alignments among multiple wheat components simultaneously
• Durum wheat 35K, 90K, 820K and TaBW280K variants
• Chromosome and centromere data can be viewed here
• AlphaFold protein predictions have been added to all transcripts - see an example here

Pangenomes

Ensembl Plants hosts the following four pangenomes:

• The barley pangenome comprises 77 wild and domesticated barley accessions
• The oat pangenome that includes 33 wild and domesticated oat lines
• The rice pangenome consists of 26 Oryza genomes including 16 Oryza sativa cultivars
• The wheat pangenome consists of 24 Triticum genomes including 19 Triticum aestivum cultivars

Archive sites

Archive of release 62 of EnsemblPlants: eg62-plants.ensembl.org (Sep 2025)

Archive of release 59 of EnsemblPlants: eg59-plants.ensembl.org (May 2024)

Archive of release 56 of EnsemblPlants: eg56-plants.ensembl.org (Feb 2023)

Archive of release 52 of EnsemblPlants: eg52-plants.ensembl.org (Dec 2021)

Funding

Ensembl Plants datasets are constructed in a direct collaboration with the Gramene resource, funded by the United States National Science Foundation award 1127112. Read more about our collaboration with Gramene.

The development of resources for wheat is funded by the BBSRC-funded Designing Future Wheat ISP and PanOryza grants.

ELIXIR implementation study FONDUE - FAIR-ification of Plant Genotyping Data and its linking to Phenotyping using ELIXIR Platforms.

Past Funding

transPLANT, funded by the European Commission within its 7th Framework Programme, under the thematic area "Infrastructures", contract number 283496.

BBSRC funding for wheat (Triticeae Genomics For Sustainable Agriculture) and barley (UK barley genome sequencing project).

ELIXIR implementation study Apple as a Model for Genomic Information Exchange.

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.