Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets
Identifieur interne : 001287 ( Main/Exploration ); précédent : 001286; suivant : 001288Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets
Auteurs : Virginie Gébelin [France] ; Xavier Argout [France] ; Worrawat Engchuan [France, Thaïlande] ; Bertrand Pitollat [France] ; Cuifang Duan [France, République populaire de Chine] ; Pascal Montoro [France] ; Julie Leclercq [France]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2012.
Abstract
Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In
Deep sequencing of small RNAs was carried out on plantlets subjected to severe abiotic stress using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and
Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs when the complete genome is not yet available. Our study provided additional information for evolutionary studies and revealed potentially specific regulation of the control of redox status in
Url:
DOI: 10.1186/1471-2229-12-18
PubMed: 22330773
PubMed Central: 3368772
Affiliations:
- France, République populaire de Chine, Thaïlande
- Languedoc-Roussillon, Occitanie (région administrative)
- Montpellier
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Le document en format XML
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<series><title level="j">BMC Plant Biology</title>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In <italic>Hevea brasiliensis</italic>
, environmental and harvesting stresses are known to affect natural rubber production. This study set out to identify abiotic stress-related miRNAs in <italic>Hevea </italic>
using next-generation sequencing and bioinformatic analysis.</p>
</sec>
<sec><title>Results</title>
<p>Deep sequencing of small RNAs was carried out on plantlets subjected to severe abiotic stress using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and <italic>Hevea </italic>
EST sequences, we identified 48 conserved miRNA families already characterized in other plant species, and 10 putatively novel miRNA families. The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families. Several <italic>MIR </italic>
genes produced both 20-22 nucleotides and 23-27 nucleotides. The two miRNA class sizes were detected for both conserved and putative novel miRNA families, suggesting their functional duality. The EST databases were scanned with conserved and novel miRNA sequences. MiRNA targets were computationally predicted and analysed. The predicted targets involved in "responses to stimuli" and to "antioxidant" and "transcription activities" are presented.</p>
</sec>
<sec><title>Conclusions</title>
<p>Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs when the complete genome is not yet available. Our study provided additional information for evolutionary studies and revealed potentially specific regulation of the control of redox status in <italic>Hevea</italic>
.</p>
</sec>
</div>
</front>
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</div1>
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</TEI>
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<li>République populaire de Chine</li>
<li>Thaïlande</li>
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<region><li>Languedoc-Roussillon</li>
<li>Occitanie (région administrative)</li>
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<settlement><li>Montpellier</li>
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</record>
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