ArticleMolecular biology and evolution2023
Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 41 citations in OpenAlex.
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- Haplotype-resolved genome ofZoological research · 2026Article
- Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus.Communications biology · 2026Article
- Uncovering the genome evolutionary dynamics of the Mediterranean endemic palm Chamaerops humilis.BMC plant biology · 2026Article
- How environment and genetic architecture of unreduced gametes shape the establishment of autopolyploids.Heredity · 2026Article
- Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes.Science advances · 2026Article
- Duplicated genes find their space: Spatial transcriptomics illuminates evolutionary fates.The Plant cell · 2025Article
- SPEECHLESS duplication in grasses expands potential for environmental regulation of stomatal development.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Gene Family Expansions Provide Molecular Flexibility Required for Context-Dependent Species Interactions.Ecology letters · 2025Article
- Article
- A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication.G3 (Bethesda, Md.) · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.Bioinformatics (Oxford, England) · 2025Article
- Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution.GigaScience · 2025Article
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Authors and funding
2 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Angiosperms have a complex history of whole-genome duplications (WGDs), with varying numbers and ages of WGD events across clades. These WGDs have greatly affected the composition of plant genomes due to the biased retention of genes belonging to certain functional categories following their duplication. In particular, regulatory genes and genes encoding proteins that act in multiprotein complexes have been retained in excess following WGD. Here, we inferred protein-protein interaction (PPI) networks and gene regulatory networks (GRNs) for seven well-characterized angiosperm species and explored the impact of both WGD and small-scale duplications (SSDs) in network topology by analyzing changes in frequency of network motifs. We found that PPI networks are enriched in WGD-derived genes associated with dosage-sensitive intricate systems, and strong selection pressures constrain the divergence of WGD-derived genes at the sequence and PPI levels. WGD-derived genes in network motifs are mostly associated with dosage-sensitive processes, such as regulation of transcription and cell cycle, translation, photosynthesis, and carbon metabolism, whereas SSD-derived genes in motifs are associated with response to biotic and abiotic stress. Recent polyploids have higher motif frequencies than ancient polyploids, whereas WGD-derived network motifs tend to be disrupted on the longer term. Our findings demonstrate that both WGD and SSD have contributed to the evolution of angiosperm GRNs, but in different ways, with WGD events likely having a more significant impact on the short-term evolution of polyploids.
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