ABSTRACT
MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.
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Acknowledgements
We thank Dr. Tom SIMS for comments on the manuscript. Dr. Zhu Kuan CHENG kindly provided the wild rice materials. This work is supported in part by a grant from Northern Illinois University Foundation to Long MAO, and National Institutes of Health (NIH) grant to Mitrick JOHNS and Long MAO (No. 44-G1A62164), and a grant from the National Natural Science Foundation of China for oversea young scholars to Long MAO (No. 30228022).
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GUDDETI, S., ZHANG, D., LI, A. et al. Molecular evolution of the rice miR395 gene family. Cell Res 15, 631–638 (2005). https://doi.org/10.1038/sj.cr.7290333
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DOI: https://doi.org/10.1038/sj.cr.7290333
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