ArticlePlant physiology2015
A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean.
Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 104 citations in OpenAlex.
- Genome-wide identification and evolution of the RCP gene family in soybean uncovers stress-responsive candidates.Functional & integrative genomics · 2026Article
- Insights into epigenetics suggest a role of DNA methylation in regulating Chinese yam tuber shape.BMC plant biology · 2026Article
- Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean.The plant genome · 2026Review
- A pangenome insight into the genome divergence and flower color diversity among Rhododendron species.BMC genomics · 2026Article
- How to improve crop pathogen resistance with epigenetics.Phytopathology research · 2026Review
- A panomics-driven framework for the improvement of major food legume crops: advances, challenges, and future prospects.Horticulture research · 2025Article
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Drought-induced transposon expression reveals complex drought response mechanisms inFrontiers in plant science · 2025Article
- Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review.Plants (Basel, Switzerland) · 2024Review
- Epigenetic variation in early and late flowering plants of the rubber-producing Russian dandelion Taraxacum koksaghyz provides insights into the regulation of flowering time.Scientific reports · 2024Article
- Evolutionary insights into 3D genome organization and epigenetic landscape ofLife science alliance · 2024Article
- Divergent evolution ofFrontiers in plant science · 2024Article
- Large-Scale Identification and Characterization Analysis ofInternational journal of molecular sciences · 2023Article
- Colchicine-Induced Polyploidy in Leguminous Crops Enhances Morpho-Physiological Characteristics for Drought Stress Tolerance.Life (Basel, Switzerland) · 2023Review
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- Polyploidy and diploidization in soybean.Molecular breeding : new strategies in plant improvement · 2023Article
- 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication.Plants (Basel, Switzerland) · 2023Article
- High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations.Molecular biology and evolution · 2023Article
- Impact of Polyploidy Induction for Salinity Stress Mitigation in Soybean (Plants (Basel, Switzerland) · 2023Review
- Role of a LORELEI- like gene from Phaseolus vulgaris during a mutualistic interaction with Rhizobium tropici.PloS one · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.
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