Origins and Evolution of MicroRNA Genes in Plant Species

Abstract

MicroRNAs (miRNAs) are among the most important regulatory elements of gene expression in animals and plants. However, their origin and evolutionary dynamics have not been studied systematically. In this paper, we identified putative miRNA genes in 11 plant species using the bioinformatic technique and examined their evolutionary changes. Our homology search indicated that no miRNA gene is currently shared between green algae and land plants. The number of miRNA genes has increased substantially in the land plant lineage, but after the divergence of eudicots and monocots, the number has changed in a lineage-specific manner. We found that miRNA genes have originated mainly by duplication of preexisting miRNA genes or protein-coding genes. Transposable elements also seem to have contributed to the generation of species-specific miRNA genes. The relative importance of these mechanisms in plants is quite different from that in Drosophila species, where the formation of hairpin structures in the genomes seems to be a major source of miRNA genes. This difference in the origin of miRNA genes between plants and Drosophila may be explained by the difference in the binding to target mRNAs between plants and animals. We also found that young miRNA genes are less conserved than old genes in plants as well as in Drosophila species. Yet, nearly half of the gene families in the ancestor of flowering plants have been lost in at least one species examined. This indicates that the repertoires of miRNA genes have changed more dynamically than previously thought during plant evolution.

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

“…MIRNA genes are generally scattered in plant genomes. Only 17% of plant MIRNA genes were found to reside within clusters, and usually fewer than three MIRNA genes are clustered together (Nozawa et al, 2012). This is in general much lower than the clustered MIRNAs in human and Drosophila spp.…”

“…These new loci may not harbor any function but could serve as the source of novel regulatory variations, which could be captured into existing networks (Cuperus et al, 2011;Nozawa et al, 2012). Therefore, young miRNAs may not necessarily have targets or may have targets that are weakly or imprecisely cleaved.…”

Prediction of potential novel microRNAs in soybean when in symbiosis

“…Furthermore, the locations of predicted candidates on the soybean genome included the intronic regions, intergenic regions, 5' and 3' untranslated regions (UTRs), and coding sequences (CDSs). Although most pre-miRNAs in plants are transcribed from the intronic and intergenic regions, they can also arise from CDSs and UTRs, as observed by Fahlgren et al (2010), Kulcheski et al (2011), andNozawa et al (2012).…”

Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs

“…To evaluate the effect of dcl3 loss of function on miRNA production, taking into account a controversy about the number of miRNA genes in C. reinhardtii (Nozawa et al 2012;Taylor et al 2014), we carried out a stringent de novo prediction of miRNAs from all the identified sRNA loci present in both wild-type and mutant-derived samples (see Methods). This prediction indicated the presence of 18 canonical miRNA loci in C. reinhardtii, named in this paper as "high confidence miRNAs" (Table 1).…”