ArticleNature communications2017
Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 182 papers, 2 of them syntheses that pooled it.
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Who cites it
182 citing papers in PubMed, 2 syntheses or guidelines pooled it, 409 citations in OpenAlex.
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
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- Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: insights into genetic diversity and function of outlier chromosomes.The Plant journal : for cell and molecular biology · 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
- Root tip excision-induced exodermis lignification impacts lateral root emergence in Brachypodium distachyon.The New phytologist · 2026Article
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- A pangenome and pantranscriptome of hexaploid oat.Nature · 2026Article
- Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding.BMC genomics · 2025Article
- An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.The Plant journal : for cell and molecular biology · 2025Article
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.Nature communications · 2025Article
- Research Progress onBiology · 2025Review
- Genome-Wide Analyses of theInternational journal of molecular sciences · 2025Article
122 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors at 13 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome 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.