Discovery of MicroRNA169 Gene Copies in Genomes of Flowering Plants through Positional Information

Calviño, Martín; Messing, Joachim

doi:10.1093/gbe/evt015

Cited by 22 publications

(13 citation statements)

References 46 publications

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“…In the present study pvu-miR166d was predicted to target kinase mRNA, which is in agreement with the reported target kinase for miR166 family in soybean [67]. Calvino and Messing [68] established that miR169 family in Sorghum targets the carboxypeptidase mRNAs. Similarly, in the present study, pvu-miR169b was predicted to target the carboxyl-terminal-processing protease.…”

Section: Discussionsupporting

confidence: 91%

Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures

et al. 2015

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BackgroundMicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99 % probability range derived from the available data.ResultsWe have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80 % sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20.ConclusionsThere is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0516-3) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 91%

Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures

et al. 2015

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“…A well-known drought-responsive miRNA, miR169, identified exclusively from control transcriptomes did not appear to accumulate in response to drought (Li et al 2008;Trindade et al 2010;Zhang et al 2011;Calviño and Messing 2013;Potkar et al 2013;Ni et al 2013;Luan et al 2014;Borowski et al 2014). Further evidence supporting the drought-related roles of this miRNA, along with two others (miR1136 and miR1137), was provided by the target analysis, in which these miRNAs were observed to bind stress-related proteins ( Fig.…”

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confidence: 85%

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

Akpınar

Kantar

Budak

2015

Funct Integr Genomics

111

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MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.

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“…It has been suggested that miR169-dependent NF-YA regulation can be involved in response to stresses in A. thaliana and maize (Leyva-Gonzalez et al 2012;Nelson et al 2007;Pant et al 2009). Its implications in fungal response in wheat (Inal et al 2014), as well as in drought tolerance and stem sugar content, were also described (Calvino and Messing 2013). Additionally, miR169 is involved in nodule development and nutritional balance in legume plants (Simon et al 2009).…”

Section: Target Predictionmentioning

confidence: 99%

Identification of apple miRNAs and their potential role in fire blight resistance

Kaja

Szcześniak

Jensen

et al. 2014

Tree Genetics & Genomes

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MicroRNAs (miRNAs) are key players in multiple biological processes; therefore, analysis and characterization of these small regulatory RNAs is a critical step toward a better understanding of animal and plant biology. In apple (Malus domestica), 200 microRNAs are known, which most probably represent only a fraction of miRNAome diversity. As a result, more effort is required to better annotate miRNAs and their functions in this economically important species. We performed deep sequencing of 12 small RNA libraries obtained for fire blight-resistant and fire blight-sensitive trees. In the sequencing results, we identified 116 novel microRNAs and confirmed a majority of previously reported apple miRNAs. We then experimentally verified selected candidates with RT-PCR and stem-loop quantitative PCR (qPCR) and performed differential expression analysis. Finally, we identified and characterized putative targets of all known apple miRNAs. The gene ontology (GO) enrichment analysis suggests prominent roles of miRNAs in response to stresses, including pathogen infection. In this study, we identified 116 new and confirmed the expression of 143 already known miRNAs. Moreover, our data suggests that apple microRNAs might be considered as regulators and markers of fire blight resistance. The analyses we performed allowed us to define four apple miRNAs potentially involved in fire blight resistance in apple trees: mdm-miR169a, mdm-miR160e, mdm-miR167b-g, and mdm-miR168a,b. These miRNAs are known to be involved in response to stresses across other plant species, usually by targeting stress response proteins. The relatively low number of candidates may result from the high variance of biological replicates and the fact that stress response miRNAs are usually induced by the stress factors and frequently expressed at a low level, or not expressed at all, in normal conditions. The results of our studies are freely available in an online database at

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Discovery of MicroRNA169 Gene Copies in Genomes of Flowering Plants through Positional Information

Cited by 22 publications

References 46 publications

Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures

Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

Identification of apple miRNAs and their potential role in fire blight resistance

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