ArticleMolecular biology and evolution2020
Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed, 122 citations in OpenAlex.
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- Chromosome-scale genome of Myriophyllum spicatum unveils the role of allohexaploidy in driving aquatic adaptation and widespread invasion.The Plant journal : for cell and molecular biology · 2026Article
- Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus.Communications biology · 2026Article
- Biosynthesis of benzylisoquinoline alkaloids and its evolution in plants.Plant communications · 2026Review
- Genome-Wide Identification and Expression Analysis of Pathogenesis-Related Protein 1 in Sweet Potato and Its Two Relatives.Food science & nutrition · 2026Article
- Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes.Science advances · 2026Article
- Genome-Wide Analysis of thePlants (Basel, Switzerland) · 2025Article
- From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean.The Plant cell · 2025Article
- The Tissue Expression Divergence of the WUSCHEL-Related Homeobox Gene Family in the Evolution of Nelumbo.Plants (Basel, Switzerland) · 2025Article
- Unveiling an ancient whole-genome duplication event in Stentor, the model unicellular eukaryotes.Science China. Life sciences · 2025Article
- Unveiling the secrets of lotus seed longevity: insights into adaptive strategies for extended storage.Journal of experimental botany · 2025Article
- Genome-wide development of simple sequence repeat (SSR) markers at 2-Mb intervals in lotus (Nelumbo Adans.).BMC genomics · 2025Article
- Divergence in MiRNA targeting of AchAco and its role in citrate accumulation in kiwifruit.BMC plant biology · 2024Article
- Genome-wide identification and analysis of ERF transcription factors related to abiotic stress responses in Nelumbo nucifera.BMC plant biology · 2024Article
- Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms.The Plant cell · 2024Article
- Pangenome Identification and Analysis of Terpene Synthase Gene Family Members inInternational journal of molecular sciences · 2024Article
- Lineage-Specific CYP80 Expansion and Benzylisoquinoline Alkaloid Diversity in Early-Diverging Eudicots.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Genome-Wide Identification and Co-Expression Networks ofPlants (Basel, Switzerland) · 2024Article
- Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication.Nature communications · 2024Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K-pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein-protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein-protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.
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