ArticleGigaScience2020
Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
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- Convergent Patterns of Karyotype Evolution Underlying Karyotype Uniformity in Conifers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.Molecular biology and evolution · 2024Article
- Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.Systematic biology · 2024Article
- Evolution of FLOWERING LOCUS T-like genes in angiosperms: a core Lamiales-specific diversification.Journal of experimental botany · 2024Article
- Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a 'diploids-first' approach to conservation.Annals of botany · 2024Article
- Demographic history inference and the polyploid continuum.Genetics · 2023Article
- The first homosporous lycophyte genome revealed the association between the recent dynamic accumulation of LTR-RTs and genome size variation.Plant molecular biology · 2023Article
- Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae.Annals of botany · 2023Article
- Article
- High-quality genome assembly ofFrontiers in microbiology · 2023Article
- Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes.GigaScience · 2022Article
- Dynamic genome evolution in a model fern.Nature plants · 2022Article
- Chromosome-Scale Genome Assembly of Gilia yorkii Enables Genetic Mapping of Floral Traits in an Interspecies Cross.Genome biology and evolution · 2022Article
- A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.Systematic biology · 2022Article
- Genome-wide identification of calcineurin B-like protein-interacting protein kinase gene family reveals members participating in abiotic stress in the ornamental woody plantFrontiers in plant science · 2022Article
- Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns.Frontiers in plant science · 2022Article
- Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions.Computational and structural biotechnology journal · 2022Review
- Underwater CAM photosynthesis elucidated by Isoetes genome.Nature communications · 2021Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundPolyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project.
resultsIn the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset.
conclusionsWe release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.
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