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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 t...
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Published in: | Functional & integrative genomics 2023-06, Vol.23 (2), p.120-120, Article 120 |
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Main Authors: | , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
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Summary: | 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. |
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ISSN: | 1438-793X 1438-7948 |
DOI: | 10.1007/s10142-023-01043-x |