Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

Abstract

To understand the expansion of multicopy microRNA (miRNA) families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miR160 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum)

“…Since the bryophytes are the most ancient land plants, this observation seems in contrast to the hypothesis that the conservation of miRNAs is the result of shared ancestry or functional convergence from an independent origin during evolution (Maher et al, 2006). One possible explanation is that miRNA genes were subjected to strong purifying selection during evolution, and that some were lost, while others experienced multiple rounds of duplication (Jiang et al, 2006;Fahlgren et al, 2007;Axtell, 2008).…”

Transcriptional Regulation of ArabidopsisMIR168aandARGONAUTE1Homeostasis in Abscisic Acid and Abiotic Stress Responses

“…To investigate how the level of miR168 is induced, we analyzed the abundance of precursor and mature miR168 under stress conditions. Given that MIR168a is ubiquitously expressed and coexpressed with AGO1 while MIR168b expression is restricted to the shoot apical meristem (Jiang et al, 2006;Gazzani et al, 2009;Vaucheret, 2009), we focused on MIR168a in this study.…”

“…To assess the role of miR168 and AGO1 in stress responses, we examined MIR168a overexpression lines (Jiang et al, 2006) and the AGO1 hypomorphic mutant allele ago1-27 (Morel et al, 2002) under ABA and abiotic stress treatments. The levels of mature miR168 in two 35S:MIR168a transgenic lines (lines 4 and 6) were more than 10-fold higher than that in the wild type, while the AGO1 transcript levels decreased to 35% and 28%, respectively, of the wild-type levels (Supplemental Fig.…”

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

“…The miR156 family of Arabidopsis also experienced a large expansion via segmental duplication events and loss of family members [16]. In addition, tandem or segmental duplication events have been shown to have had a role in evolution of other miRNA families in rice, such as miR160, miR162, miR167, miR169, miR171 and miR395 [17,18]. Therefore, as for protein-coding genes, duplication and loss of duplicates may represent one of the main evolutionary routes for birth and death of MIRNAs in plants.…”

“…It was found that duplication events played an important role in diversification and evolution of these miRNA families [16]. Duplication was also one of the main mechanisms involved in the evolution of several rice miRNA families, such as the miR159 and miR395 families [17,18]. Of 12 miR156 family members located on six chromosomes, miR156b and miR156c (miR156b/c hereafter) are tandem miRNAs on chromosome 1.…”