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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	Properties
	CanonicalTranscript.rds	6.5MB	2020-08-03 05:47
	FunctionalAnnotation.rds	5.5MB	2020-08-03 05:47
	HCTriads.csv	3.0MB	2020-08-03 05:47
	MeanTpms.rds	503MB	2020-08-03 05:47
	NonSyntenicTriads.csv	161KB	2020-08-03 05:47
	Non_syn_TriadMovement.rds	179KB	2020-08-03 05:47
	Non_syn_Triads.rds	3.9MB	2020-08-03 05:47
	ObservedGOTermsWithSlim.csv	2.0MB	2020-08-03 05:47
	OntologiesForGenes.rds	65MB	2020-08-03 05:47
	SegmentalTriads.csv	3.0MB	2020-08-03 05:47
	TriadMovement.rds	23MB	2020-08-03 05:47
	Triads.rds	392MB	2020-08-03 05:47
	WGCNA_table.csv	32MB	2020-08-03 05:47
	expressed_genes_tpmsOver0.5AtLeast8Samples.csv	6.8MB	2020-08-03 05:47
	id_names_merged.txt	2.5MB	2020-08-03 05:47
	metadata.csv	168KB	2020-08-03 05:47
	motifs.rds	330MB	2020-08-03 05:47
	region_partition.csv	564 B	2020-08-03 05:47
	samples_to_use.csv	107KB	2020-08-03 05:47
	universe_table.csv	28MB	2020-08-03 05:47
	wheat.homeolog_groups.release.full_set.csv.gz	1.0MB	2020-08-03 05:47

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