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MicroRNAs (miRNAs) participate in various vitally biological processes via controlling target genes activity and thousands of miRNAs have been identified in many species to date, including 18,698 known animal miRNA in miRBase. However, there are only limited studies reported in rainbow trout (Oncorhynchus mykiss) especially via the computational-based approaches. In present study, we systematically investigated the miRNAs in rainbow trout using a well-developed comparative genome-based homologue search. A total of 196 potential miRNAs, belonging to 124 miRNA families, were identified, most of which were firstly reported in rainbow trout. The length of miRNAs ranged from 17 to 24 nt with an average of 20 nt while the length of their precursors varied from 47 to 152 nt with an average of 85 nt. The identified miRNAs were not evenly distributed in each miRNA family, with only one member per family for a majority, and multiple members were also identified for several families. Nucleotide U was dominant in the pre-miRNAs with a percentage of 30.04%. The rainbow trout pre-miRNAs had relatively high negative minimal folding free energy (MFE) and adjusted MFE (AMFE). Not only the mature miRNAs but their precursor sequences are conserved among the living organisms. About 2466 O. mykiss genes were predicted as potential targets for 189 miRNAs. Gene Ontology (GO) analysis showed that nearly 2093, 2107, and 2081 target genes are involved in cellular component, molecular function, and biological processes respectively. KEGG pathway enrichment analysis illuminated that these miRNAs targets might regulate 105 metabolic pathways, including those of purine metabolism, nitrogen metabolism, and oxidative phosphorylation. This study has provided an update on rainbow trout miRNAs and their targets, which represents a foundation for future studies. 相似文献
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Characterization of the rainbow trout egg microRNA transcriptome 总被引:1,自引:0,他引:1
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Prediction and identification of herpes simplex virus 1-encoded microRNAs 总被引:14,自引:0,他引:14
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Cui C Griffiths A Li G Silva LM Kramer MF Gaasterland T Wang XJ Coen DM 《Journal of virology》2006,80(11):5499-5508
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MicroRNAs (miRNAs) are small RNAs, generally of 20–23 nt, that down-regulate target gene expression during development, differentiation,
growth, and metabolism. In Populus, extensive studies of miRNAs involved in cold, heat, dehydration, salinity, and mechanical stresses have been performed;
however, there are few reports profiling the miRNA expression patterns during pathogen stress. We obtained almost 38 million
raw reads through Solexa sequencing of two libraries from Populus inoculated and uninoculated with canker disease pathogen. Sequence analyses identified 74 conserved miRNA sequences belonging
to 37 miRNA families from 154 loci in the Populus genome and 27 novel miRNA sequences from 35 loci, including their complementary miRNA* strands. Intriguingly, the miRNA*
of three conserved miRNAs were more abundant than their corresponding miRNAs. The overall expression levels of conserved miRNAs
increased when subjected to pathogen stress, and expression levels of 33 miRNA sequences markedly changed. The expression
trends determined by sequencing and by qRT-PCR were similar. Finally, nine target genes for three conserved miRNAs and 63
target genes for novel miRNAs were predicted using computational analysis, and their functions were annotated. Deep sequencing
provides an opportunity to identify pathogen-regulated miRNAs in trees, which will help in understanding the regulatory mechanisms
of plant defense responses during pathogen infection. 相似文献
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Genome organization and characteristics of soybean microRNAs 总被引:3,自引:0,他引:3
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To identify novel as well as conserved miRNAs in citrus, deep sequencing of small RNA library combined with microarray was
performed in precocious trifoliate orange (an early flowering mutant of trifoliate orange, Poncirus trifoliata L. Raf.), resulting in the obtainment of a total of 114 conserved miRNAs belonging to 38 families and 155 novel miRNAs. The
miRNA star sequences of 39 conserved miRNAs and 27 novel miRNAs were also discovered among newly identified miRNAs, providing
additional evidence for the existence of miRNAs. Through degradome sequencing, 172 and 149 genes were identified as targets
of conserved miRNAs and novel miRNAs, respectively. GO and KEGG annotation revealed that high ranked miRNA-target genes were
those implicated in biological and metabolic processes. To characterize those miRNAs expressed at the juvenile and adult development
stages of citrus, further analysis on the expression profiles of these miRNAs through hybridizing the commercial microarray
and real-time PCR was performed. The results revealed that some miRNAs were down-regulated at adult stage compared with juvenile
stage. Detailed comparison of the expression patterns of some miRNAs and corresponding target genes revealed the negative
correlation between them, while few of them are positively correlated. 相似文献
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Background
To date, several studies have indicated a major role for microRNAs (miRNAs) in regulating plant development, but miRNA-mediated regulation of the developing somatic embryo is poorly understood, especially during early stages of somatic embryogenesis in hardwood plants. In this study, Solexa sequencing and miRNA microfluidic chips were used to discover conserved and species-specific miRNAs during somatic embryogenesis of hybrid yellow poplar (Liriodendron tulipifera×L. chinense).Methodology/Principal Findings
A total of 17,214,153 reads representing 7,421,623 distinct sequences were obtained from a short RNA library generated from small RNAs extracted from all stages of somatic embryos. Through a combination of deep sequencing and bioinformatic analyses, we discovered 83 sequences with perfect matches to known miRNAs from 33 conserved miRNA families and 273 species-specific candidate miRNAs. MicroRNA microarray results demonstrated that many conserved and species-specific miRNAs were expressed in hybrid yellow poplar embryos. In addition, the microarray also detected another 149 potential miRNAs, belonging to 29 conserved families, which were not discovered by deep sequencing analysis. The biological processes and molecular functions of the targets of these miRNAs were predicted by carrying out BLAST search against Arabidopsis thaliana GenBank sequences and then analyzing the results with Gene Ontology.Conclusions
Solexa sequencing and microarray hybridization were used to discover 232 candidate conserved miRNAs from 61 miRNA families and 273 candidate species-specific miRNAs in hybrid yellow poplar. In these predicted miRNAs, 64 conserved miRNAs and 177 species-specific miRNAs were detected by both sequencing and microarray hybridization. Our results suggest that miRNAs have wide-ranging characteristics and important roles during all stages of somatic embryogenesis in this economically important species. 相似文献17.
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Paolo Martini Gabriele Sales Mattia Brugiolo Alessandro Gandaglia Filippo Naso Cristiano De Pittà Michele Spina Gino Gerosa Francesco Chemello Chiara Romualdi Stefano Cagnin Gerolamo Lanfranchi 《PloS one》2014,9(4)