Abstract
Although RNA silencing has been studied primarily in model plants, advances in high-throughput sequencing technologies have enabled profiling of the small RNA components of many more plant species, providing insights into the ubiquity and conservatism of some miRNA-based regulatory mechanisms. Small RNAs of 20 to 24 nucleotides (nt) are important regulators of gene transcript levels by either transcriptional or by posttranscriptional gene silencing, contributing to genome maintenance and controlling a variety of developmental and physiological processes. Here, we used deep sequencing and molecular methods to create an inventory of the small RNAs in the mangrove species, Avicennia marina. We identified 26 novel mangrove miRNAs and 193 conserved miRNAs belonging to 36 families. We determined that 2 of the novel miRNAs were produced from known miRNA precursors and 4 were likely to be species-specific by the criterion that we found no homologs in other plant species. We used qRT-PCR to analyze the expression of miRNAs and their target genes in different tissue sets and some demonstrated tissue-specific expression. Furthermore, we predicted potential targets of these putative miRNAs based on a sequence homology and experimentally validated through endonucleolytic cleavage assays. Our results suggested that expression profiles of miRNAs and their predicted targets could be useful in exploring the significance of the conservation patterns of plants, particularly in response to abiotic stress. Because of their well-developed abilities in this regard, mangroves and other extremophiles are excellent models for such exploration.
Highlights
Small 20–24 nucleotides non-coding RNAs are important regulators of gene expression, causing either transcriptional gene silencing (TGS) or posttranscriptional gene silencing (PTGS) [1,2,3]
One strand of the processed small RNA duplex subsequently associates with an Argonaute family protein and is incorporated into an RNAinduced silencing complex (RISC) that scans for nucleic acids complementary to the loaded small RNA to execute its function [34,35,36,37]
The majority of the mangrove silencing small RNAs obtained in this study were 24 nt in size, accounting for 35% of silencing small RNAs, followed by 21 nt (16%), 23 nt (12%), 20 nt (10%), and 22 nt (8%) (Figure 1). This result was consistent with those reported for other plant species, including A. thaliana, M. truncatula, O. sativa, P. trichocarpa, A. hypogaea, and C. trifoliate [13,15,18,21,23,25]
Summary
Small 20–24 nucleotides (nt) non-coding RNAs are important regulators of gene expression, causing either transcriptional gene silencing (TGS) or posttranscriptional gene silencing (PTGS) [1,2,3]. They were first described in Caenorhabditis elegans [4] and were subsequently found to be responsible for RNA interference (RNAi), co-suppression, gene silencing, quelling and plant PTGS [5,6,7,8,9]. RNA slicing and translational repression control gene expression post-transcriptionally, whereas histone modification and DNA methylation inhibit gene expression at the transcriptional level
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