ArticleNature communications2025
De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Nonadditive gene expression and reduced homoeolog expression bias in an intraspecific hexaploid wheat hybrid.BMC plant biology · 2026Article
- Allelic expression and subgenome bias influence plant height in cultivated hybrid sugarcane.aBIOTECH · 2026Article
- Toward telomere-to-telomere genomics in Fabaceae: Unlocking comparative and functional insights into symbiotic nitrogen fixation.Cell genomics · 2026Review
- Advances in gene cloning and functional genomics approaches for wheat (Triticum aestivum L.) improvement.The plant genome · 2026Review
- Toward a model of repeat-driven chromosomal fragility in Triticeae: an integrated structural omics perspective.BMC genomics · 2026Review
- Rewiring diversity, physiology, and practice: integrating the next decade of wheat science.Journal of experimental botany · 2026Article
- The potential of wheat spatial omics.Nature genetics · 2026Review
- A pangenome and pantranscriptome of hexaploid oat.Nature · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement.Nature communications · 2025Article
- De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.Nature communications · 2025Article
- Improvement of simultaneous genome editing of homoeologous loci in polyploid wheat using CRISPR/Cas9 applying tRNA processing system.Plant biotechnology (Tokyo, Japan) · 2025Article
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Authors and funding
42 authors.
Funding
Abstract
Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. We utilise both the newly constructed gene-based wheat pan-genome and pan-transcriptome, demonstrating variation in the prolamin superfamily and immune-reactive proteins across cultivars.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.