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

Abstract

It has been shown that overexpression of MIR156b/c resulted in a bushy phenotype in maize and rice. Our results indicated that the MIR156b/c locus was highly conserved among cereals, but not in dicots and that genome duplication events played an important role in the evolution of the miR156 family. Genetic diversity investigation at the locus indicated that only $9% of nucleotide diversity observed in wild rice (O. rufigogon) was maintained in the cultivated rice and the neutral model was rejected (P < 0.05) based on Tajima's D and Fu and Li's D * and F * tests. To our knowledge, this is the first example of miRNA gene to be targeted by both natural and domestication selection in plants.

A Genome-Wide Characterization of MicroRNA Genes in Maize

“…MicroRNA loci may control such fundamental processes in development that alterations of sequence or expression are not tolerated. Our results are similar to studies in Arabidopsis [107],[108] and rice [35] where strong purifying selection has acted on the mature miRNA, whereas flanking regions generally reflect species wide diversity levels.…”

“…Two members of the miRNA156 family (miR156b and miR156c) on chromosome 3 are separated by less than 200nt, as are two members of the miRNA166 family on chromosome 5. The close distance of miR156b and miR156c is observed in several monocots and they are transcribed as one transcript (polycistronic) in maize [24] and rice [35]. Clusters of two members of miR166 are also observed in several plant species, including moss [33]–[37].…”

Overexpression of the maizeCorngrass1microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass

“…Cg1 is a unique tandem miR156 microRNA gene that, to date, has been identified only in grass species (7) and may have been under purifying selection during domestication (30). The unique structure of this gene may play a role in transcript stability because the full-length Cg1 transcript can be easily detected on RNA blots (7) in contrast to many miR156 precursors.…”

Genomic analysis of rice microRNA promoters and clusters

“…Also, this process implies that the co-transcription of functionally different miRNAs in a cluster may simultaneously target several categories of genes (Guddeti et al, 2005;Wang et al, 2007). In contrast, some other miRNA clusters demonstrate the independent and transcriptional regulation and relative long-distance physical location (Tanzer and Stadler, 2004).…”