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.
Highlights
MicroRNAs are key regulators of gene expression and play important roles in many aspects of plant biology
We previously identified a number of soybean miRNAs through high throughput sequencing of a small RNA library and examining WGS and EST sequences for potential precursors [18]
We speculated that when the complete genome sequence of soybean is available, additional novel miRNAs might be discovered
Summary
MicroRNAs (miRNAs) are key regulators of gene expression and play important roles in many aspects of plant biology. MiRNA* is generally degraded and the mature miRNA molecule is incorporated into a RNA-induced silencing complex (RISC), composed of different proteins including the catalytic protein ARGONAUTE (AGO). This complex either directs the cleavage of complementary target mRNAs [2,3,6] or inhibits their translation [7] primarily depending on the extent of sequence complementarity between the miRNA and the target mRNA. MiRNAs play crucial roles in many aspects of plant development including organ morphogenesis or patterning primarily by regulating hormone signaling [3,7]. They play a role in response to abiotic stresses [1214] and resistance against pathogenic organisms [15]
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