Index of /under_license/toronto/Ramirez-Gonzalez_etal_2018-06025-Transcriptome-Landscape/expvip/TGACv1 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	Properties
	.DS_Store	6.0KB	2020-08-03 05:46
	Aneuploidy_summary.tsv	834 B	2020-08-03 05:47
	CS_methylome_summary.tsv	1.0KB	2020-08-03 05:46
	CS_spike_summary.tsv	327 B	2020-08-03 05:46
	DRP000768_summary.tsv	435 B	2020-08-03 05:47
	Development_summary.tsv	7.3KB	2020-08-03 05:46
	ERP003465_summary.tsv	2.0KB	2020-08-03 05:46
	ERP004505_summary.tsv	1.0KB	2020-08-03 05:46
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	ERP015130_summary.tsv	595 B	2020-08-03 05:47
	ERP016738_summary.tsv	260 B	2020-08-03 05:46
	PAMP Triggered Imune Response_summary.tsv	826 B	2020-08-03 05:46
	SRP004884_summary.tsv	279 B	2020-08-03 05:46
	SRP013449_summary.tsv	245 B	2020-08-03 05:46
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	SRP045409_summary.tsv	531 B	2020-08-03 05:46
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	SRP060670_summary.tsv	244 B	2020-08-03 05:46
	SRP064598_summary.tsv	355 B	2020-08-03 05:46
	SRP067916_summary.tsv	217 B	2020-08-03 05:46
	SRP068156_summary.tsv	530 B	2020-08-03 05:46
	SRP068165_summary.tsv	878 B	2020-08-03 05:46
	SRP078208_summary.tsv	321 B	2020-08-03 05:46
	Triticum_aestivum_CS42_TGACv1_scaffold.annotation.gff3.cdna.fa.gz	117MB	2020-08-03 05:46
	choulet_URGI_summary.tsv	1.2KB	2020-08-03 05:46
	compara_homolgy_32_85.txt	13MB	2020-08-03 05:46
	developing spike_summary.tsv	3.1KB	2020-08-03 05:47
	ByGene/		2020-08-03 05:46
	ByTranscript/		2020-08-03 05:46

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