ArticleGenome biology2015
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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Who cites it
70 citing papers in PubMed, 1 synthesis or guideline pooled it, 115 citations in OpenAlex.
- Transcriptome meta-analysis of abiotic stresses-responsive genes and identification of candidate transcription factors for broad stress tolerance in wheat.Protoplasma · 2023Pooled it
- Genetic dissection of cold stress tolerance and yield potential under cold stress in nested synthetic wheat (Triticum aestivum L.) introgression libraries using multi-locus genome-wide association and haplotype analysis.Functional & integrative genomics · 2026Article
- A Genome-Wide Pseudogene Map Reveals the Asymmetric Evolution of the A, B, and D Subgenomes in Common Wheat.Plants (Basel, Switzerland) · 2026Article
- Genome-Wide Association Analysis and Candidate Gene Prediction of Wheat Wet Gluten Content.International journal of molecular sciences · 2026Article
- Genome-wide association study and KASP marker development for flour color in winter wheat.Scientific reports · 2025Article
- Heavy Metal-Associated (HMA) Domain-Containing Proteins: Insight into Their Features and Roles in Bread Wheat (Biology · 2025Article
- Impact of structural variations and genome partitioning on bread wheat hybrid performance.Functional & integrative genomics · 2025Article
- Deciphering drought-response in wheat (Frontiers in plant science · 2025Article
- Investigation of two-pore KHeliyon · 2024Article
- Genome wide characterization and expression analysis ofFrontiers in plant science · 2024Article
- Plant Tolerance to Drought Stress with Emphasis on Wheat.Plants (Basel, Switzerland) · 2023Review
- Fine mapping of KLW1 that conditions kernel weight mainly through regulating kernel length in wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- A computational study on the structure-function relationships of plant caleosins.Scientific reports · 2023Article
- Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (Plant signaling & behavior · 2022Article
- Article
- Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number.Plants (Basel, Switzerland) · 2022Article
- Wheat transcriptomic responses to extended feeding by wheat curl mites.Scientific reports · 2022Article
- Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat (Life (Basel, Switzerland) · 2022Article
- Article
- Molecular Characterization, Evolutionary Analysis, and Expression Profiling ofPlants (Basel, Switzerland) · 2022Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBecause of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before.
resultsBy combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level.
conclusionsOur analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.
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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.