The transcriptional landscape of hexaploid wheat across tissues, cultivars, and stress conditions

Ricardo Ramirez-Gonzalez, Philippa Borrill, Cristobal Uauy
The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world?s major crops. However, the balance of homoeolog expression across diverse tissues, stress conditions, and cultivars remains poorly understood. Here we combine extensive gene expression datasets with the fully annotated genome sequence to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varied between tissues, with ~30% of wheat homoeologs showing unbalanced expression. We found expression asymmetries along wheat chromosomes, with genes showing the largest inter-tissue, inter-cultivar, and coding sequence variation most often located in the high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps towards neo/sub- functionalization of wheat homoeologs. Co-expression networks revealed extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in polyploid wheat. Project Code: BB/P016855/1
This data is made available under the Toronto Agreement
All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement. By using this data, you agree to:
  • respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
  • not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.
  • contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.
  • fully cite the prepublication data along with any applicable versioning details.
  • understand that this data as accessed is precompetitive and is not patentable in its present state.
This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.
      Search:

          User details

          You are browsing the public view on the public zone
          NameSizeDateProperties
          iRods Data ObjectAneuploidy_count.tsv.gz9.4MB2020-08-03 05:44
          iRods Data ObjectAneuploidy_tpm.tsv.gz 12MB2020-08-03 05:44
          iRods Data ObjectCS_methylome_count.tsv.gz6.2MB2020-08-03 05:45
          iRods Data ObjectCS_methylome_tpm.tsv.gz7.8MB2020-08-03 05:45
          iRods Data ObjectCS_spike_count.tsv.gz5.3MB2020-08-03 05:45
          iRods Data ObjectCS_spike_tpm.tsv.gz7.2MB2020-08-03 05:44
          iRods Data ObjectDRP000768_count.tsv.gz4.8MB2020-08-03 05:44
          iRods Data ObjectDRP000768_tpm.tsv.gz6.1MB2020-08-03 05:44
          iRods Data ObjectDevelopment_count.tsv.gz 73MB2020-08-03 05:44
          iRods Data ObjectDevelopment_tpm.tsv.gz 95MB2020-08-03 05:44
          iRods Data ObjectERP003465_count.tsv.gz 26MB2020-08-03 05:44
          iRods Data ObjectERP003465_tpm.tsv.gz 32MB2020-08-03 05:44
          iRods Data ObjectERP004505_count.tsv.gz9.0MB2020-08-03 05:45
          iRods Data ObjectERP004505_tpm.tsv.gz 12MB2020-08-03 05:44
          iRods Data ObjectERP008767_count.tsv.gz3.3MB2020-08-03 05:45
          iRods Data ObjectERP008767_tpm.tsv.gz4.0MB2020-08-03 05:44
          iRods Data ObjectERP009837_count.tsv.gz 12MB2020-08-03 05:45
          iRods Data ObjectERP009837_tpm.tsv.gz 15MB2020-08-03 05:44
          iRods Data ObjectERP013829_count.tsv.gz 28MB2020-08-03 05:45
          iRods Data ObjectERP013829_tpm.tsv.gz 36MB2020-08-03 05:45
          iRods Data ObjectERP013983_count.tsv.gz 12MB2020-08-03 05:44
          iRods Data ObjectERP013983_tpm.tsv.gz 16MB2020-08-03 05:44
          iRods Data ObjectERP015130_count.tsv.gz5.5MB2020-08-03 05:45
          iRods Data ObjectERP015130_tpm.tsv.gz7.3MB2020-08-03 05:45
          iRods Data ObjectERP016738_count.tsv.gz3.0MB2020-08-03 05:44
          iRods Data ObjectERP016738_tpm.tsv.gz3.8MB2020-08-03 05:45
          iRods Data ObjectPAMP_Triggered_Imune_Response_count.tsv.gz8.1MB2020-08-03 05:45
          iRods Data ObjectPAMP_Triggered_Imune_Response_tpm.tsv.gz 11MB2020-08-03 05:44
          iRods Data ObjectSRP004884_count.tsv.gz3.7MB2020-08-03 05:44
          iRods Data ObjectSRP004884_tpm.tsv.gz4.2MB2020-08-03 05:44
          iRods Data ObjectSRP013449_count.tsv.gz2.8MB2020-08-03 05:45
          iRods Data ObjectSRP013449_tpm.tsv.gz3.4MB2020-08-03 05:45
          iRods Data ObjectSRP017303_count.tsv.gz1.1MB2020-08-03 05:45
          iRods Data ObjectSRP017303_tpm.tsv.gz1.1MB2020-08-03 05:45
          iRods Data ObjectSRP022869_count.tsv.gz3.1MB2020-08-03 05:44
          iRods Data ObjectSRP022869_tpm.tsv.gz4.0MB2020-08-03 05:45
          iRods Data ObjectSRP028357_count.tsv.gz 42MB2020-08-03 05:45
          iRods Data ObjectSRP028357_tpm.tsv.gz 51MB2020-08-03 05:44
          iRods Data ObjectSRP029372_count.tsv.gz2.3MB2020-08-03 05:44
          iRods Data ObjectSRP029372_tpm.tsv.gz3.1MB2020-08-03 05:45
          iRods Data ObjectSRP038912_count.tsv.gz2.2MB2020-08-03 05:45
          iRods Data ObjectSRP038912_tpm.tsv.gz2.5MB2020-08-03 05:44
          iRods Data ObjectSRP041017_count.tsv.gz6.6MB2020-08-03 05:44
          iRods Data ObjectSRP041017_tpm.tsv.gz9.0MB2020-08-03 05:44
          iRods Data ObjectSRP041022_count.tsv.gz5.9MB2020-08-03 05:44
          iRods Data ObjectSRP041022_tpm.tsv.gz6.7MB2020-08-03 05:44
          iRods Data ObjectSRP043554_count.tsv.gz3.1MB2020-08-03 05:45
          iRods Data ObjectSRP043554_tpm.tsv.gz3.7MB2020-08-03 05:44
          iRods Data ObjectSRP045409_count.tsv.gz5.9MB2020-08-03 05:45
          iRods Data ObjectSRP045409_tpm.tsv.gz7.7MB2020-08-03 05:45
          iRods Data ObjectSRP048912_count.tsv.gz 16MB2020-08-03 05:44
          iRods Data ObjectSRP048912_tpm.tsv.gz 22MB2020-08-03 05:44
          iRods Data ObjectSRP056412_count.tsv.gz 25MB2020-08-03 05:44
          iRods Data ObjectSRP056412_tpm.tsv.gz 35MB2020-08-03 05:44
          iRods Data ObjectSRP060670_count.tsv.gz2.6MB2020-08-03 05:45
          iRods Data ObjectSRP060670_tpm.tsv.gz3.3MB2020-08-03 05:44
          iRods Data ObjectSRP064598_count.tsv.gz4.7MB2020-08-03 05:45
          iRods Data ObjectSRP064598_tpm.tsv.gz5.3MB2020-08-03 05:44
          iRods Data ObjectSRP067916_count.tsv.gz2.6MB2020-08-03 05:45
          iRods Data ObjectSRP067916_tpm.tsv.gz3.2MB2020-08-03 05:44
          iRods Data ObjectSRP068156_count.tsv.gz6.5MB2020-08-03 05:45
          iRods Data ObjectSRP068156_tpm.tsv.gz8.2MB2020-08-03 05:44
          iRods Data ObjectSRP068165_count.tsv.gz6.6MB2020-08-03 05:45
          iRods Data ObjectSRP068165_tpm.tsv.gz7.7MB2020-08-03 05:44
          iRods Data ObjectSRP078208_count.tsv.gz3.6MB2020-08-03 05:45
          iRods Data ObjectSRP078208_tpm.tsv.gz4.5MB2020-08-03 05:45
          iRods Data Objectchoulet_URGI_count.tsv.gz 12MB2020-08-03 05:45
          iRods Data Objectchoulet_URGI_tpm.tsv.gz 16MB2020-08-03 05:44
          iRods Data Objectdeveloping_spike_count.tsv.gz 17MB2020-08-03 05:45
          iRods Data Objectdeveloping_spike_tpm.tsv.gz 23MB2020-08-03 05:44