ArticleNucleic acids research2014
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Diploid- and tetraploid wall barley exhibit alternative molecular responses but comparable reproductive performance in response to different ambient temperature regimes.The Plant journal : for cell and molecular biology · 2026Article
- Remodeling of homoeolog expression bias buffers stress response in allotetraploid cotton.BMC plant biology · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- A likelihood ratio test for detecting shifts in homeolog expression ratios in allopolyploids.The New phytologist · 2026Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation.Nature genetics · 2025Article
- Transcriptional dynamics during karyogamy in rice zygotes.Development (Cambridge, England) · 2025Article
- Wheat Cybrid Plants, OryzaWheat, Regenerated from Wheat-Rice Hybrid Zygotes via in Vitro Fertilization System Possess Wheat-Rice Hybrid Mitochondria.Plant & cell physiology · 2024Article
- Review
- Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility.Nature communications · 2023Article
- Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation.Nature communications · 2023Article
- A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat.NAR genomics and bioinformatics · 2023Article
- Detection of Transcription Factors Related to Axillary Bud Development after Exposure to Cold Conditions in HexaploidPlants (Basel, Switzerland) · 2023Article
- Low impact of polyploidization on the transcriptome of synthetic allohexaploid wheat.BMC genomics · 2023Article
- The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits.Plant communications · 2023Article
- Article
- Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.Molecular biology and evolution · 2022Article
- Subgenome dominance and its evolutionary implications in crop domestication and breeding.Horticulture research · 2022Article
- Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the InvasiveFrontiers in genetics · 2022Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.
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