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


[ 1 ] Instytut Informatyki, Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ P ] employee

Scientific discipline (Law 2.0)

[2.3] Information and communication technology
[7.5] Biological sciences

Year of publication


Published in

Functional and Integrative Genomics

Journal year: 2023 | Journal volume: vol. 23 | Journal number: iss. 2

Article type

scientific article

Publication language


  • MicroRNA
  • miRNA
  • Copy number variation
  • Expression
  • Transposons

EN MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) 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 MIRs—which are MIRs 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) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs 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 MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.

Date of online publication


Pages (from - to)

120-1 - 120-16





Article Number: 120

License type

CC BY (attribution alone)

Open Access Mode

czasopismo hybrydowe

Open Access Text Version

final published version

Date of Open Access to the publication

at the time of publication

Ministry points / journal


Impact Factor

2.9 [List 2022]

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