Arabidopsis thaliana cultivar:CVI-0 Raw sequence reads
Plant genomes must be dynamic to cope with heterogeneous selective pressures across their natural landscapes. Genomic variation in the model plant A. thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focussing on Single Nucleotide Polymorphisms (SNPs). Conversely, Structural variations have been largely overlooked in spite of their likely dramatic effect on phenotype. Here we identified 167,298 indels and structural variants ranging in size from 1bp to 10 kb including presence/absence variants (PAVs), inversions and tandem duplications among 1301 A. thaliana natural accessions. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes. Our results further suggest that defense-related genes (R-genes, secondary metabolites) and F-box genes have an excess of PAVs compared to other genes. We find an excess of intermediate frequency PAVs in defense response genes in nearly all populations, consistent with a history of balancing selection on this class of genes. Finally, we find that multiple genic PAVs are associated with maximum and minimum temperatures at collection sites, suggesting roles in local adaptation through vernalization (cold requirement for flowering) and drought response.