In silicon prediction of conserved miRNAs in Leguminosae and their gains and losses during evolutionary process

Leguminosae is one of the most important plant families. In this study, we searched Arachis hypogaea, Glycine max, G. soja, Lotus japonicas, Medicago truncatula, Phaseolus vulgaris, and Vigna unguiculata conserved miRNAs through Expressed Sequence Tag (EST) based-homology method. All candidate sequences with appropriate fold-back structures were screened and characterized according to several filtering criteria. Chromosomal MIR locus and their distributions determined. The Dollo maximum parsimony was employed to construct the species relationship based on the MIR birth and death. Also, the number of MIRs gains and losses in the evolutionary process. In addition, we estimated the numbers of MIRs in their ancestral species using Dollo maximum parsimony in their phylogenetic tree. We found 414 novel miRNAs from 130 MIR families meeting the restricted filtering criteria. Either evolutionary time or the number of miRNAs gains and losses are estimated and characterized in the ancestral species based on the taxon-based phylogenetic tree. It speculates that gains of miRNA gene families within Leguminosae have accelerated during its evolutionary time. In addition, several taxon-specific MIR families find to assign diverse taxon and their species. Our thorough analyses resulted in the definition of some miRNA families as being lineage-specific. Therefore, they can use as markers in future systematic studies.