Wheat Genomics Resources at Ensembl Plants

Ensembl Plants is an integrated portal for accessing genomic data for plant species, via an interactive genome browser, programmatic (Perl and REST-ful APIs), FTP, and a data mining tool (BioMart). The latest release includes the genomes of 12 cereal genomes including the diploid progenitors of the bread wheat A and D genomes and the bread wheat chromosome survey sequence generated by the IWGSC.  In addition to sequence assemblies and gene models, a number of additional data sets have been aligned to the survey sequence, including the complete genomes of  Brachypodium and rice, wheat unigene clusters  from NCBI, and wheat RNA-seq data deposited in the INSDC archives.  The wheat genome assemblies previously generated by Brenchley et al. (PMID: 23192148) have also been aligned to the survey sequence, Brachypodium and barley; and homeolegous SNPs inferred between the 3 wheat genomes are also displayed.  Additionally, the evolutionary history of each protein-coding gene annotated on the survey sequence has been inferred from comparisons to other species, and gene trees and protein alignments are available to browse and download.  Finally, sequence search is available against the wheat assemblies, gene models, and ESTs; and functional annotation inferred using GO, InterPro and homology metrics.  Future work will focus on increasing the range of comparative analyses and sequence alignments, the extension of the existing comparative analysis framework to better display the 3 wheat genomes in the context of each other, and the development of new resources for homeologeous and varietal SNPs.