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

Abstract

BackgroundIntraspecies 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.ResultsWe 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.ConclusionsWe 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 materialThe online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.

Copy Number Variation in Domestication

“…CNVs formed by this mechanism are characterized by tracts of homology on either side of the CNV. NAHR is common in repetitive regions and an important source of tandem duplications and deletions [8]. Another mechanism is single-strand annealing (SSA), which is a doublestrand break repair process where broken ends are joined by annealing at homologies >30 bp in length, which can result in significant deletions [6] ( Figure 1B).…”

Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant‐parasitic nematode Meloidogyne incognita

“…In recent years, whole‐genome sequencing has shown that besides point mutations, copy number variations (CNVs) constitute another important mechanism of genomic variation submitted to selection. This feature has been identified in most model organisms across the plant or animal kingdom (Brown et al., ; Locke et al., ; Yu et al., ; Zmienko, Samelak‐Czajka, Kozlowski, & Figlerowicz, ) and consists of DNA segments typically exceeding 1 kb that are variable in copy number in comparison with a reference genome, share a sequence identity higher than 95% and are dispersed throughout the genome (Alkan, Coe, & Eichler, ). CNVs can either be inherited from the previous generation or appear de novo through duplication/deletion events, and their fixation by drift or selection may contribute to the creation of genetic novelty resulting in species adaptation to stressful or novel environments (Katju & Bergthorsson, ; Kondrashov, ).…”

A Chromosome-level Sequence Assembly Reveals the Structure of theArabidopsis thalianaNd-1 Genome and its Gene Set

“…However, it is impossible to unequivocally distinguish between real genes and pseudogenes in all cases, because even genes with a premature stop codon or a frameshift mutation could function as a truncated versions or give rise to regulatory RNAs [73, 76–78]. In addition, the impact of copy number variations involving protein encoding genes in A. thaliana might be higher than previously assumed thus supporting the existence of multiple gene copies [79]. Gene expression analysis could support the discrimination of pseudogenes, because low gene expression in A. thaliana was reported to be associated with pseudogenization [80].…”