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. the existence of highly conserved miRNAs and siRNAs with important regulatory functions PD 0332991 Isethionate manufacture in both plants and animals [27], [28]. Small RNAs are derived from partially double-stranded RNA (dsRNA) precursors by the action of ribonuclease III-family enzymes designated Dicers and Dicer-like (DCL) proteins [3], [29]. The small RNA duplexes generated by Dicer activity have a characteristic 2-nucleotide overhang at the 3 end due to offset cleavage of the complementary strands by Dicers and DCLs. In plants these 3 overhangs are stabilised PD 0332991 Isethionate manufacture by 2-O-methylation [30]C[33]. One strand of the processed small RNA duplex subsequently associates with an Argonaute family protein and is incorporated into an RNA-induced silencing complex (RISC) that scans for nucleic acids complementary to the loaded small RNA to execute its function [34]C[37]. In plants, small RNAs act to silence genes by mediating RNA cleavage [38]C[41], translational repression [42]C[44], histone modification and DNA methylation [2], [45], [46]. RNA slicing and translational repression control gene expression post-transcriptionally, whereas histone modification and DNA methylation inhibit gene expression at the transcriptional level. Dominating tropical intertidal zones and estuaries and evolutionarily adapted to tolerate flooding, anoxia, high temperatures, wind, and high and extremely variable salt conditions in typically resource-poor environments, PRKM12 mangrove ecosystems are comprised of halophytes, predominantly trees [47]C[50]. There are about 20 million hectares of mangroves in Asia, Oceania, Africa, the Americas and the Middle East [51]C[53]. Mangroves play an important role in coastal protection, maintenance of water quality and biodiversity [50]. Generally, mangrove forests are heavily exploited due to excessive wood gathering, fishpond operations, mining, and development of coastal areas and disposal of pollutants [50]. PD 0332991 Isethionate manufacture Mangroves exhibit several physiological strategies for handling salt, ranging from salt excretion (e.g., annotated miRNAs identified in this study were subjected to gene ontology (GO) analysis to identify gene functions. Materials and Methods Ethics Statement No specific permits were required for the described field study. No specific permissions were required for this location and activities. The location is not privately-owned or protected in anyway and the field studies did not involve endangered or protected species. Plant Materials and RNA Isolation Mangrove (and 5 adapter: PD 0332991 Isethionate manufacture 5-GUUCAGAGUUCUACAGUCCGACGAUC-3) were ligated to each end of the RNA molecule and a reverse-transcription (RT) reaction was carried out to generate single-stranded cDNA using RT primer (and database (Rfam 11.0) [57] and plant repeat databases to discard abundant non-coding RNAs (rRNA, tRNA, snRNA, and snoRNA) or mRNAs degradation products (http://rfam.sanger.ac.uk/and http://plantrepeats.plantbiology.msu.edu/). We performed a BLASTN search on each unique sequence remaining after the filtering steps against known mature and precursor miRNAs (pre-miRNAs) from other plant species deposited in the miRBase database (http://www.mirbase.org/) [58]. Only perfectly matched sequences were considered to be conserved miRNAs. Conserved miRNAs PD 0332991 Isethionate manufacture having perfect matches to mangrove cDNA sequences (deposited in the Mangrove Transcriptome Database (MTDB), http://mangrove.illinois.edu, a web-based platform providing transcriptome information from 28 mangrove species [55]) were subjected to stem-loop structure prediction using web server (http://mfold.rna.albany.edu/?q=mfold) [59]. Predictions were made using RNA sequences containing 50C200 nucleotides on either side of the candidate miRNA. In case no apparent local foldback structure was predicted for a given sequence, larger upstream and downstream sequences were submitted for analysis. The criteria used to identify candidate structured precursors were those suggested by [60]. Target genes of the miRNAs were predicted using the online tool gene (accession no. “type”:”entrez-nucleotide”,”attrs”:”text”:”Y17766″,”term_id”:”5514638″,”term_text”:”Y17766″Y17766) was used as reference gene for normalization. All reactions were run in triplicate. The primers for subsequent real time PCR reactions are reported in Table S1. Detection of miRNA Target Cleavage Products Synthesis of 5 RACE-ready cDNAs was carried out using the BD Smart RACE cDNA amplification kit (CLONTECH, USA). Subsequent PCR reactions were performed using the UPM Primer-Mix supplied with the kit in combination with gene-specific primers derived from miRNA target genes (Table S1). Amplification products corresponding to the size of the expected cleavage products were then gel-purified, cloned and sequenced. Gene Ontology Analysis To identify miRNA target functions and classifications, as well as the metabolic regulatory networks associated with mangrove miRNAs and their.