ArticleNature genetics2025
A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- N-glycosylation code diversifies paralogous chitinases to balance plant immunity and growth.Nature plants · 2026Article
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- Molecular integration of seasonal temperature signals in flowering time control.Nature reviews. Genetics · 2026Review
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea.Nature communications · 2026Article
- Article
- Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon.Nature genetics · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Structural variation in context: mechanisms, functions and selection regimes across the tree of life.Heredity · 2026Article
- Genomics in wheat improvement: Progress and perspectives.The plant genome · 2026Review
- Regulatory Mechanisms Underlying Stem Strength and Toughness in Dicotyledonous Plants: Implications for Soybean Breeding.Current issues in molecular biology · 2026Review
- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Variability in drought gene expression datasets highlights the need for paired physiology and community standardization.Plant physiology · 2026Article
- Identification of genome size and heterozygosity in 510 Jujube (Frontiers in plant science · 2026Article
- Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana.Nature plants · 2025Article
- Article
- Pangenomes as a framework for adaptive radiation, speciation, and adaptation.American journal of botany · 2025Article
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Authors and funding
27 authors.
Funding
Abstract
Making sense of whole-genome polymorphism data is challenging, but it is essential for overcoming the biases in SNP data. Here we analyze 27 genomes of Arabidopsis thaliana to illustrate these issues. Genome size variation is mostly due to tandem repeat regions that are difficult to assemble. However, while the rest of the genome varies little in length, it is full of structural variants, mostly due to transposon insertions. Because of this, the pangenome coordinate system grows rapidly with sample size and ultimately becomes 70% larger than the size of any single genome, even for n = 27. Finally, we show how short-read data are biased by read mapping. SNP calling is biased by the choice of reference genome, and both transcriptome and methylome profiling results are affected by mapping reads to a reference genome rather than to the genome of the assayed individual.
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