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Published on February 27, 2008; 10.1104/pp.108.116582

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Received January 20, 2008
Accepted February 19, 2008

Sequence variation of microRNAs and their binding sites in Arabidopsis thaliana

Ian M. Ehrenreich * and Michael D. Purugganan

Department of Biology and Center for Comparative Functional Genomics, New York University, New York, New York 10003; Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695

* Corresponding author; email: ehrenreich{at}ncsu.edu.

Major differences exist between plants and animals both in the extent of miRNA-based gene regulation and the sequence complementarity requirements for miRNA-mRNA pairing. Whether these differences affect how these sites evolve at the molecular level is unknown. To determine the extent of sequence variation at miRNAs and their targets in a plant species, we re-sequenced 16 miRNA families (66 miRNAs in total) and all 52 of the characterized binding sites for these miRNAs in the plant model Arabidopsis thaliana, accounting for around 50 percent of the known miRNAs and binding sites in this species. As has been shown previously in humans, we find that both miRNAs and their target binding sites have very low nucleotide variation and divergence compared to their flanking sequences in A. thaliana, indicating strong purifying selection on these sites in this species. Sequence data flanking the mature miRNAs, however, exhibit normal levels of polymorphism for the accessions in this study and, in some cases, non-neutral evolution or subtle effects on predicted pre-miRNA secondary structure, suggesting that there is raw material for the differential function of miRNA alleles. Overall, our results show that despite differences in the architecture of miRNA-based regulation, miRNAs and their targets are similarly constrained in both plants and animals.




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J. de Meaux, J.-Y. Hu, U. Tartler, and U. Goebel
Structurally different alleles of the ath-MIR824 microRNA precursor are maintained at high frequency in Arabidopsis thaliana
PNAS, July 1, 2008; 105(26): 8994 - 8999.
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