ArticleNature communications2023
The pan-genome and local adaptation of Arabidopsis thaliana.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed, 119 citations in OpenAlex.
- Structural variant detection across sequencing technologies.Nature biotechnology · 2026Article
- Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding.Journal of integrative plant biology · 2026Article
- Structural variation in the IAMH2 3' UTR underlies hypocotyl elongation during light adaptation in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2026Article
- Integrated pangenomics and population genomics reveal climate adaptation and maladaptation in an East Asian tree.Nature communications · 2026Article
- Article
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Predictive models of the genetic bases underlying budding yeast fitness in multiple environments.NAR genomics and bioinformatics · 2026Article
- Dovetailing the Genetic, Developmental and Functional Bases of the Adaptation of Stomatal Traits to Climate.Ecology letters · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Stepwise allelic trajectory of ETP2 underlies trade-off between UVB tolerance and submergence adaptation in Arabidopsis thaliana.Nature communications · 2026Article
- Natural variation modifies centromere-proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana.Genetics · 2026Article
- A single species, different repeatomes? Genomic plasticity in Passiflora foetida L. complex and comparative insights across the subgenus Passiflora.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Allelic variation of an LRR only protein confers dual pathogen resistance in Arabidopsis.Nature communications · 2026Article
- Dual-SVF: a robust knowledge-guided multimodal method for structural variant filtering in long-read sequencing.Briefings in bioinformatics · 2026Article
- RNA i-motif landscapes in plant kingdom and their potential functional roles.Molecular biology and evolution · 2026Article
- Comprehensive genomic analysis and database construction for Apiales.Journal of advanced research · 2026Article
- Integration of structural variation enhances the resolution of population structure and helps delineate conservation units.Annals of botany · 2026Article
- Genome-wide CG hypomethylation of theProceedings of the National Academy of Sciences of the United States of America · 2026Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.
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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.