Identification and characterization of miRNAs and their potential targets in flax

Neutelings, Godfrey; Fénart, Stéphane; Lucau-Danila, Anca; Hawkins, Simon

doi:10.1016/j.jplph.2012.06.011

Cited by 43 publications

(38 citation statements)

References 60 publications

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“…The lengths of these identified mature miRNA sequences ranged from 19 to 24 nucleotides; however, most of the potential miRNAs (17 of 27 or 62.96%) were 21 nt in length (Table 1). This length was quite similar to other mature miRNAs already identified in other plants (Zhang et al, 2006a;Xie et al, 2010;Barozai et al, 2012;Neutelings et al, 2012). The A+U contents of these predicted P. vulgaris pre-miRNA sequences ranged from 30.34 to 68.37%, with an average of 57.95 ± 8.53% (Table 1), which closely matched the results of previous studies (Ambros et al, 2003;Neutelings et al, 2012).…”

Section: Identification Of Potential Mirnassupporting

confidence: 88%

“…The identified P. vulgaris pre-miRNAs were between 68 and 202 nt in length, with an average of 111.37 ± 34.17 nt; however, the majority of the pre-miRNAs (24 of 27 or 88.89%) were 60-150 nt in length (Table 1). These results matched the lengths of most previously predicted premiRNAs in plant species (Zhang et al, 2007;Unver and Budak, 2009;Barozai et al, 2012;Neutelings et al, 2012). Although the identified P. vulgaris miRNA precursors were of a wide range of lengths, they could be folded into the typical miRNA secondary structures (Figure 2).…”

Section: Identification Of Potential Mirnassupporting

confidence: 85%

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Computational identification of miRNAs and their targets in Phaseolus vulgaris

jinsoo¹,

Xie²,

Kong³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. MicroRNAs (miRNAs) are a class of non-coding small RNAs that negatively regulate gene expression at the posttranscriptional level. Although thousands of miRNAs have been identified in plants, limited information is available about miRNAs in Phaseolus vulgaris, despite it being an important food legume worldwide. The high conservation of plant miRNAs enables the identification of new miRNAs in P. vulgaris by homology analysis. Here, 1804 known and unique plant miRNAs from 37 plant species were blast-searched against expressed sequence tag and genomic survey sequence databases to identify novel miRNAs in P. vulgaris. All candidate sequences were screened by a series of miRNA filtering criteria. Finally, we identified 27 conserved miRNAs, belonging to 24 miRNA families. When compared against known miRNAs in P. vulgaris, we found that 24 of the 27 miRNAs were newly discovered. Further, we identified 92 potential target genes with known functions for these novel miRNAs. Most of these target genes were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress response. The identification of the novel miRNAs in P. vulgaris is anticipated to

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Section: Identification Of Potential Mirnassupporting

confidence: 88%

Section: Identification Of Potential Mirnassupporting

confidence: 85%

Computational identification of miRNAs and their targets in Phaseolus vulgaris

jinsoo¹,

Xie²,

Kong³

et al. 2014

Genet. Mol. Res.

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“…It was shown that miR408 was also responsive to phosphate limitation and became more abundant during phosphate limitation (Pant et al, 2009). Functions of lus-miR408 predicted targets in flax were metabolism, transport and transcription factor (Neutelings et al, 2012). In our study we observed miR408 up-regulation induced by Pi deficiency, and this could indicate that this miRNA takes part in expression regulation during mineral nutrient stress in flax.…”

Section: Mir408 Up-regulation In Flax Under Pi Deficiencysupporting

confidence: 56%

“…In Arabidopsis miR398 is up-regulated during copper deficiency (Zhu et al, 2011) and down-regulated under N starvation conditions (Liang, He, & Yu, 2012). Lus-miR398 targets were predicted in flax; their functions were: metabolism, signaling, transport and transcription factor (Neutelings, Fenart, Lucau-Danila, & Hawkins, 2012;Barvkar et al, 2013). In our investigation of flax miRNAs, the up-regulation of miR398 under nutrient deficiency was observed.…”

Section: Role Of Mir398 In Flax Pi Homeostasis Regulationmentioning

confidence: 67%

Flax Inorganic Phosphate Deficiency Responsive miRNAs

Melnikova¹,

Belenikin²,

Bolsheva³

et al. 2013

JAS

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MicroRNAs (miRNAs) control a variety of biological processes and are involved in plant response to abiotic stress including phosphate starvation. Phosphate deficiency is one of the major limiting factors for crop yield. In the present work inorganic phosphate deficiency responsive miRNAs were identified in flax for the first time by high-throughput sequencing. Three conserved miRNA families (miR398, miR399 and miR408) were differentially expressed under inorganic phosphate starvation. In other plant species it was demonstrated that these miRNAs are involved in response to a combination of different stresses. In phosphate starvation conditions miR399 and miR408 are up-regulated but miR398 is differentially expressed. We found that in flax under inorganic phosphate starvation stress conditions expression level alterations for conserved miRNAs miR399 and miR408 were close to those in other plant species and for miR398 -to those in tomato but not in Arabidopsis. A better understanding of miRNAs stress regulatory functions would provide new tools for genetic improvement of stress tolerance in flax and other plants.

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“…The NormFinder analysis, which considers the intra-and intergroup variation of gene expression, identified the gm-miR171a as the top ranking house-keeping gene. The miR168 belongs to the group of potential biomarkers of plant stress response (Bej and Basak, 2014;Neutelings et al, 2012). Under different types of abiotic stress (drought, salinity, cold, UV, mechanical, and heat stress), up-regulation of miR168 expression (Bej and Basak, 2014;Sunkar, 2010) has been observed.…”

Section: Characterisation Of Selected Mirnamentioning

confidence: 99%

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

Ražná¹,

Hlavačková

Bežo

et al. 2015

Acta fytotechn zootechn

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Two types of molecular markers based on randomly amplified DNA by RAPD-based assay and amplified microRNA by miRNA-based assay were applied for the genotyping of five accessions of Silybum marianum (L.) Gaertn. It was also verified the effectiveness of the isolation of genomic DNA by three commercially available isolation kits and two similar complex methods and their applicability for this medicinal herb. None of the commercial isolation kits provided the genomic DNA of sufficient quality and quantity. Applied originally designed CTAB method and modified CTAB method for purpose of DNA isolation from medicinal plants allowed to isolate DNA of required quality and of sufficient yield. RAPD-based DNA fingerprints, allowed to distinguish the individual genotypes of Silybum marianum. MicroRNA-based markers showed the cross-genera transferability potential and displayed sufficient level of polymorphism. Both types of molecular markers could be used as suitable tool for genotyping of milk thistle. However, because of the size of miRNA amplicons is the efficiency of miRNA-based markers PCR amplifications preferred and consequently less DNA quality-dependent which may be advantageous in view of the content of undesirable secondary metabolites in medicinal plants.

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Identification and characterization of miRNAs and their potential targets in flax

Cited by 43 publications

References 60 publications

Computational identification of miRNAs and their targets in Phaseolus vulgaris

Computational identification of miRNAs and their targets in Phaseolus vulgaris

Flax Inorganic Phosphate Deficiency Responsive miRNAs

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

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