ArticleMolecular biology and evolution2021
A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 41 citations in OpenAlex.
- Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Functional insights into dispensable genes using genome-wide loss-of-function burden tests in Arabidopsis.The Plant cell · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- A simple method to efficiently generate structural variation in plants.PLoS genetics · 2025Article
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Next-generation translational genomics for developing future crops.Functional & integrative genomics · 2025Review
- Article
- Construction of the super pan-genome for the genusHorticulture research · 2025Article
- Previously unmeasured genetic diversity explains part of Lewontin's paradox in abioRxiv : the preprint server for biology · 2024Article
- Article
- A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.Nature genetics · 2024Article
- kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS.G3 (Bethesda, Md.) · 2023Article
- The pan-genome and local adaptation of Arabidopsis thaliana.Nature communications · 2023Article
- The role of gene presence-absence variations on genetic incompatibility in Asian rice.The New phytologist · 2023Article
- Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.Genome biology · 2023Article
- Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.Plant biotechnology journal · 2023Article
- Predicting phenotypes from novel genomic markers using deep learning.Bioinformatics advances · 2023Article
- Prioritized candidate causal haplotype blocks in plant genome-wide association studies.PLoS genetics · 2022Article
- The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights.Annals of botany · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a "core" genome underlying basic cellular processes and a "flexible" genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.
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