Data mining for miRNAs and their targets in the Triticeae

Dryanova, A.; Zakharov, Arseny ZakharovA.; Gulick, Patrick J.

doi:10.1139/g08-025

Cited by 56 publications

(63 citation statements)

References 29 publications

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“…Therefore, one should expect that these miRNAs should be functional. This approach was successfully used for the identification of new miRNAs in plants (Zhang et al 2005;Yao et al 2007;Dryanova et al 2008;Sunkar and Jagadeeswaran 2008;Zhou et al 2008;Unver and Budak 2009). miRNA sequences of main monocot species with the greatest number of registered miRNAs were used in blast analysis.…”

Section: Discussionmentioning

confidence: 99%

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Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

2017

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As an essential regulatory component in plants, microRNAs (miRNAs) have been intensively studied over the past decade. Although hundreds of miRNAs have been identified and analyzed in many important crops and model plants, very little is known about the function of common wheat (Triticum aestivum L.) miRNAs. In this study, we performed computational prediction of novel wheat miRNAs based on BLAST searches of the expressed sequence tag database. The expression profiles of all miRNAs were performed for both vegetative and reproductive tissues to identify developmentally regulated miRNAs. A total of 19 new miRNAs belonging to 12 MIR families were identified using stringent criteria for miRNA annotation. For all of the miRNAs, the secondary structures of their precursor sequences were predicted. Two pairs of distinct miRNAs were found to be located on the same precursor. The predicted miRNAs were experimentally verified by a stemloop qRT-PCR-based assay. The expression profiles were performed in both vegetative and reproductive tissues to find the potential correlations between the developmental phase and miRNA activity. Thirteen out of 19 miRNAs were upregulated at certain phases of plant development, and three of them (miR319, miR395, and miR171) showed the greatest expression in young spikes during microsporogenesis. Our results provide useful information for future studies of miRNA-mediated regulation of flower and grain development in wheat.

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Section: Discussionmentioning

confidence: 99%

“…The putative miRNA sequences are then validated based on criteria proposed for miRNA annotation. Although only conserved miRNAs can be found by blast searches, the vast amount of plant miRNAs have been identified by this strategy (Yao et al 2007;Dryanova et al 2008;Sunkar and Jagadeeswaran 2008;Zhou et al 2008).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

2017

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“…Considering that computational approaches or high-throughput sequencing have identified many wheat miRNAs, the mature sequences of the 34 identified miRNAs were compared with published data for miRNAs (Yao et al, 2007;Dryanova et al, 2008;Jin et al, 2008;�an et al, 2009;Wei et al, 2009). BLAST results show that 27 miRNAs have identical sequence with previously reported miRNAs in wheat.…”

Section: Identification Of Conserved Mirnas In Wheatmentioning

confidence: 99%

Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum)

Yin¹,

Shen²

2010

Genet. Mol. Res.

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ABSTRACT. MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression by translational repression or transcript degradation. A large number of miRNAs have been identified from model plant species; however, the character of conserved miRNAs is poorly understood. We studied 42 miRNA families that are conserved within the plant kingdom, using the miRBase database. Some conserved miRNA families were found to be preferentially expressed in dicots relative to monocots, especially miR403, miR472 and miR479. Using an improved homology search-based approach and the conserved miRNAs as the query set, 34 conserved miRNAs and the miR482 family were identified in wheat. Forty-six wheat mRNAs were predicted as their putative target genes. Most conserved wheat miRNAs were found to retain homologous target interactions and have analogous molecular functions. The miR172 displayed a wheat-specific function and was found to have an additional target interaction with succinyl-CoA ligase. We concluded that although miRNAs are conserved, the expression and function of some have drifted during long periods of plant evolution.

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“…In this study, 62 potential wheat miRNAs belonging to 30 miRNA families were identified. Given that many wheat miRNAs have been identified by high-throughput sequencing or computational approaches, the mature sequences of the 62 identified miRNAs were compared with published wheat miRNAs (Yao et al, 2007;Dryanova et al, 2008;Jin et al, 2008;Han et al, 2009;Wei et al, 2009;Yin and Shen, 2010). The results indicated that 14 miRNAs had an identical sequence with previously reported wheat miRNAs, including miR159, miR169, miR171, miR319, miR395a-c, miR398, miR408, miR444, miR1120, miR1128, and miR1135.…”

Section: Identification Of Potential Wheat Mirnas By Est Analysismentioning

confidence: 98%

Identification of miRNAs and their targets in wheat (Triticum aestivum L.) by EST analysis

Han¹,

Kong²,

Xie³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. MicroRNAs (miRNAs) are a newly discovered class of noncoding small RNAs that regulate gene expression by directing target mRNA cleavage or translational inhibition. A large number of miRNAs have been identified in plants. Increasing evidence has shown that miRNAs play multiple roles in plant biological processes. So far, identification of miRNAs has been limited to a few model plant species, whose genomes have been sequenced. Wheat (Triticum aestivum L.) is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat. Here, we showed the conserved miRNAs identified in wheat by expressed sequence tag (EST) analysis. All previously known miRNAs from Arabidopsis, rice, and other plant species were used in a BLAST search against the wheat EST database to identify novel wheat miRNAs by a series of filtering criteria. By this strategy, we identified 62 conserved miRNAs, belonging to 30 miRNA families, 48 of which were newly discovered in wheat. These newly identified wheat miRNAs may regulate 287 potential targets, which are involved in development, signal transduction, metabolic pathways, disease resistance, ion transportation, and environmental stress response.

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Data mining for miRNAs and their targets in the Triticeae

Cited by 56 publications

References 29 publications

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum)

Identification of miRNAs and their targets in wheat (Triticum aestivum L.) by EST analysis

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