Investigation on the Conserved MicroRNA Genes in Higher Plants

Analysis of evolving microRNA repertoires within the plant domain can further corroborate our understanding of genome evolution and plasticity. An extensive collection of relatively unbiased miRBase-registered plant miRNAs and predicted unlistedMIRs from 23 plant ESTs were examined. As a result, 4324 pre-miRNAs were predicted and classified in 656 miRNA gene families with mostly being transposons (57.81%). From 216 newly identified pre-miRNAs, 103 distinct types belonged to reduced complexity/repeated regions. Collinearity between the numbers of miRNAs in each species with the relevant sizes of genomes was absent. Duplications ofMIRs were evident, with higher MIR paralogs in Liliopsida compared with dicots. Due to the lack of an apparent pattern of phylogeny, Dollo maximum parsimony was used that established the acceleration of gains and potential losses of miRNA gene families within Mesangiospermae during the last 200 million years ago. Phylogenetic analysis of Liliopsida in contrast to Eudicotyledons agreed with the reconstructed tree based on the possible expansion of distinguished MIR families. In marked contrast to dicots, the degrees of resemblance in Liliopsida were higher than their direct predecessors. Analyses of recent monophyletic lineages were illustrative of miRNA horizontal genes transfer.