Arabidopsis thaliana cultivar:CVI-0 Raw sequence reads. Arabidopsis thaliana cultivar:CVI-0

Genomic variation in the model plant A. thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single nucleotide polymorphisms (SNPs). 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 1bp to 10 kb, including presence/absence variants (PAVs), inversions and tandem duplications in 1301 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.