Genome organization and characteristics of soybean microRNAs

Abstract

BackgroundmicroRNAs (miRNAs) are key regulators of gene expression and play important roles in many aspects of plant biology. The role(s) of miRNAs in nitrogen-fixing root nodules of leguminous plants such as soybean is not well understood. We examined a library of small RNAs from Bradyrhizobium japonicum-inoculated soybean roots and identified novel miRNAs. In order to enhance our understanding of miRNA evolution, diversification and function, we classified all known soybean miRNAs based on their phylogenetic conservation (conserved, legume- and soybean-specific miRNAs) and examined their genome organization, family characteristics and target diversity. We predicted targets of these miRNAs and experimentally validated several of them. We also examined organ-specific expression of selected miRNAs and their targets.ResultsWe identified 120 previously unknown miRNA genes from soybean including 5 novel miRNA families. In the soybean genome, genes encoding miRNAs are primarily intergenic and a small percentage were intragenic or less than 1000 bp from a protein-coding gene, suggesting potential co-regulation between the miRNA and its parent gene. Difference in number and orientation of tandemly duplicated miRNA genes between orthologous genomic loci indicated continuous evolution and diversification. Conserved miRNA families are often larger in size and produce less diverse mature miRNAs than legume- and soybean-specific families. In addition, the majority of conserved and legume-specific miRNA families produce 21 nt long mature miRNAs with distinct nucleotide distribution and regulate a more conserved set of target mRNAs compared to soybean-specific families. A set of nodule-specific target mRNAs and their cognate regulatory miRNAs had inverse expression between root and nodule tissues suggesting that spatial restriction of target gene transcripts by miRNAs might govern nodule-specific gene expression in soybean.ConclusionsGenome organization of soybean miRNAs suggests that they are actively evolving. Distinct family characteristics of soybean miRNAs suggest continuous diversification of function. Inverse organ-specific expression between selected miRNAs and their targets in the roots and nodules, suggested a potential role for these miRNAs in regulating nodule development.

Two MicroRNAs Linked to Nodule Infection and Nitrogen-Fixing Ability in the Legume Lotus japonicus

“…Different studies have shown that, in addition to a set of evolutionarily conserved miRNAs found across phyla, plants including legumes possess lineage-or species-specific miRNAs of more recent evolutionary origin (He et al, 2008;Szittya et al, 2008;LelandaisBrière et al, 2009;Cuperus et al, 2011;Peláez et al, 2012;Turner et al, 2012). To identify new miRNAs in L. japonicus, we used the plant de novo miRNA prediction algorithm miRCat Supplemental Fig.…”

“…To date, a large number of miRNA families have been described in legumes, many of which are conserved beyond this lineage and also occur in Arabidopsis (Arabidopsis thaliana), as evidenced in the miRBase registry (www.mirbase.org; Subramanian et al, 2008;Jagadeeswaran et al, 2009;Lelandais-Brière et al, 2009;Joshi et al, 2010;Chi et al, 2011;Devers et al, 2011;Li et al, 2011;Peláez et al, 2012;Turner et al, 2012). Furthermore, symbiosis-responsive sRNAs have also recently been identified at different stages of nodule development (Subramanian et al, 2008;Jagadeeswaran et al, 2009;Lelandais-Brière et al, 2009;Li et al, 2010;Kulcheski et al, 2011), including several miRNAs found to be highly expressed in nodules (LelandaisBrière et al, 2009;Wang et al, 2009).…”

Clock-Controlled and FLOWERING LOCUS T (FT)-Dependent Photoperiodic Pathway inLotus japonicusII: Characterization of a MicroRNA Implicated in the Control of Flowering Time

“…there are at least four genes encoding miR172, although no biological experiment has been carried out with regard to the physiological functions of these putative genes. 36) Hence we decided to identify genes for miR172 in L. japonicus and characterize the function of them. The hallmark of the miR172 gene is its final product of a short RNA strand of 21 bases, 5 0 -AGAAUCUUGAUG-CUGCAU-3…”

Gene Duplication and RNA Silencing in Soybean

“…Melito et al have used amiRNA to downregulate the leucine-rich repeat transmembrane receptor-kinase gene in soybean [99]. miRNA has been extensively studied in soybean [127][128][129][130], information of which may be useful for designing amiRNAs. Because of its specificity, this method will be useful for silencing a limited copy of duplicated genes in soybean.…”