Index of /under_license/toronto/Ramirez-Gonzalez_etal_2018-06025-Transcriptome-Landscape/scripts/TEs on public

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

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Name	Size	Date
TE_Family_Comparison_10-80-10_Movement_UPLOAD.R	3.7KB	2020-08-03 05:47
calculate_sliding_windows_TEs.r	4.8KB	2020-08-03 05:47
get_average_length_of_TEs_and_distance_to_ATG.r	17KB	2020-08-03 05:47
plot_final_TE_density_graphs.r	10KB	2020-08-03 05:47
retro_presenceabsence_subsetting_analysis_dominancecategories_with1500_UPLOAD.R	11KB	2020-08-03 05:47
retro_presenceabsence_subsetting_analysis_movementcategories_with1500_UPLOAD.R	8.8KB	2020-08-03 05:47

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