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 unlisted MIRs 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 of MIRs 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.

Small RNAs (sRNAs) that do not get untranslated into proteins exhibit a pivotal role in the expression regulation of their cognate gene(s) in almost all eukaryotic lineages, including plants. Hitherto, numerous protein families such as Dicer, a unique class of Ribonuclease III, have been reported to be involved in sRNAs processing pathways and silencing. In this study, we aimed to investigate the phylogenetic relationship and evolutionary history of the DCL protein family. Our results illustrated the DCL family of proteins grouped into four main subfamilies (DCLs 1–4) presented in either Eudicotyledons or Liliopsids. The accurate observation of the phylogenetic trees supports the independent expansion of DCL proteins among the Eudicotyledons and Liliopsids species. They share the common origin, and the main duplication events for the formation of the DCL subfamilies occurred before the Eudicotyledons/Liliopsids split from their ancestral DCL. In addition, shreds of evidence revealed that the divergence happened when multicellularization started and since the need for complex gene regulation considered being a necessity by organisms. At that time, they have evolved independently among the monophyletic lineages. The other finding was that the combination of DCL protein subfamilies bears several highly conserved functional domains in plant species that originated from their ancestor architecture. The conservation of these domains happens to be both lineage-specific and inter lineage-specific. DCL subfamilies (i.e., DCL1-DCL4) distribute in their single clades after diverging from their common ancestor and before emerging into higher plants. Therefore, it seems that the main duplication events for the formation of the DCL subfamilies occurred before the Eudicotyledons/Liliopsida split and before the appearance of moss, and after the single-cell green algae. We also observed the same trends among the main DCL subfamilies from functional unit composition and architecture. Despite the long evolutionary course from the divergence of Liliopsida lineage from the Eudicotyledons, a significant diversifying force to domain composition and orientation was absent. The results of this study provide a deeper insight into DCL protein evolutionary history and possible sequence and structural relationships between DCL protein subfamilies in the main higher plant monophyletic lineages; i.e., Eudicotyledons and Liliopsida.