ArticleGenome biology and evolution2016
Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 59 citations in OpenAlex.
- Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates.Genome biology and evolution · 2026Article
- Using reciprocally retained gene families to detect whole-genome multiplications in plants.Genome biology · 2026Article
- Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes.Science advances · 2026Article
- From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean.The Plant cell · 2025Article
- Whole Genome Duplication in the Genomics Era: The Hidden Gems in Invertebrates?Genome biology and evolution · 2025Review
- Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms.The Plant cell · 2024Article
- Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis inInternational journal of molecular sciences · 2023Article
- Revisiting ancient polyploidy in leptosporangiate ferns.The New phytologist · 2023Article
- A Comprehensive Study of the WRKY Transcription Factor Family in Strawberry.Plants (Basel, Switzerland) · 2022Article
- Convergent evolution of polyploid genomes from across the eukaryotic tree of life.G3 (Bethesda, Md.) · 2022Article
- Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns.Frontiers in plant science · 2022Article
- Grape Small Auxin Upregulated RNA (International journal of molecular sciences · 2021Article
- An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis).Horticulture research · 2021Article
- The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event.Systematic biology · 2021Article
- Evolutionary diversification of cytokinin-specific glucosyltransferases in angiosperms and enigma of missing cis-zeatin O-glucosyltransferase gene in Brassicaceae.Scientific reports · 2021Article
- Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii).Scientific reports · 2021Article
- Model-Based Detection of Whole-Genome Duplications in a Phylogeny.Molecular biology and evolution · 2020Article
- Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions.GigaScience · 2020Article
- Article
- Loss ofFrontiers in plant science · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that the genomes of all angiosperms have experienced at least two ancient WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost. Thus, it can be extremely difficult to identify, let alone characterize, ancient WGDs. In this study, we use a new maximum likelihood estimator to test for evidence of ancient WGDs in land plants and estimate the fraction of new genes copies that are retained following a WGD using gene count data, the number of gene copies in gene families. We identified evidence of many putative ancient WGDs in land plants and found that the genome fractionation rates vary tremendously among ancient WGDs. Analyses of WGDs within Brassicales also indicate that background gene duplication and loss rates vary across land plants, and different gene families have different probabilities of being retained following a WGD. Although our analyses are largely robust to errors in duplication and loss rates and the choice of priors, simulations indicate that this method can have trouble detecting multiple WGDs that occur on the same branch, especially when the gene retention rates for ancient WGDs are very low. They also suggest that we should carefully evaluate evidence for some ancient plant WGD hypotheses.
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