ArticleNature communications2020
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
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Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 citations in OpenAlex.
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- Chromosome-level Streptochaeta genome elucidates the ancestral karyotype and allopolyploid origin of grasses.Nature communications · 2026Article
- A Palearctic divide, niche conservatism and host-fungal endophyte interactions shaped the phylogeography of the grassPlant diversity · 2026Article
- Drivers of insect herbivory resistance and tolerance to plant damage in the Brachypodium distachyon species complex.American journal of botany · 2026Article
- Plastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection.BMC plant biology · 2026Article
- The genetic structure of aPeerJ · 2026Article
- The polyploid continuum and the landscape of polyploid genomic variation.American journal of botany · 2025Review
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Near-complete genome assembly of allotetraploid Erianthus rockii reveals unique chromosome evolution and lineage-divergence trajectories in the Saccharum complex.Plant communications · 2025Article
- Transposon Dynamics Drive Genome Evolution and Regulate Genetic Mechanisms of Agronomic Traits in Cotton.Plants (Basel, Switzerland) · 2025Article
- Thriving or Withering? Plant Molecular Cytogenetics in the First Quarter of the 21st Century.International journal of molecular sciences · 2025Review
- Genomic and evolutionary evidence for drought adaptation of allopolyploid Brachypodium hybridum.Journal of experimental botany · 2025Article
- Diploidization in a wild rice allopolyploid is both episodic and gradual.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation.Nature genetics · 2025Article
- Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza.The New phytologist · 2025Article
- The developments and prospects of plant super-pangenomes: Demands, approaches, and applications.Plant communications · 2025Review
- Does time matter? Intraspecific diversity of ribosomal RNA genes in lineages of the allopolyploid model grass Brachypodium hybridum with different evolutionary ages.BMC plant biology · 2024Article
- Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon.Genetics · 2024Article
- Pangenome analysis reveals transposon-driven genome evolution in cotton.BMC biology · 2024Article
- The evolution of transposable elements ineLife · 2024Article
Corrections and comments
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Authors and funding
33 authors at 10 institutions in 10 countries.
Funding
Abstract
Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.