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Background  Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant  Arabidopsis thaliana  at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted.    Results  We analyzed the natural CNVs in the region overlapping  MSH2  gene that encodes the DNA mismatch repair protein, and  AT3G18530  and  AT3G18535  genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189  A. thaliana  accessions. We found that  AT3G18530  and  AT3G18535  were duplicated (2–14 times) in 20 and deleted in 101 accessions.  MSH2  was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the  MSH2  duplications were associated with those of  AT3G18530  and  AT3G18535 . Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with  AT3G18530  and  AT3G18535  deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV.    Conclusions  We characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding  MSH2 ,  AT3G18530  and  AT3G18535  genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular insight into the mechanism underlying the recurrent nature of  AT3G18530 - AT3G18535  duplications/deletions. We also performed the first direct comparison of the two leading experimental methods, suitable for assessing the DNA copy number status. Our comprehensive case study provides foundation information for further analyses of CNV evolution in Arabidopsis and other plants, and their possible use in plant breeding.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.

bmc genomics

Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location