Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes

MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes ( MIR s) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIR s—which are MIR s restricted to one plant family, genus, or even species—are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIR s in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIR s were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIR s presented moderate variation. Transposon-derived MIR s displayed exceptionally high diversity. Conversely, MIR s involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIR s. Our data indicate that CNV rate of Arabidopsis MIR s is related with their age, function, and genomic localization.