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Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets.

Gébelin V, Argout X, Engchuan W, Pitollat B, Duan C, Montoro P, Leclercq J - BMC Plant Biol. (2012)

Bottom Line: The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families.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 Hevea.

View Article: PubMed Central - HTML - PubMed

Affiliation: CIRAD, UMR AGAP, F-34398 Montpellier, France.

ABSTRACT

Background: 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 Hevea brasiliensis, environmental and harvesting stresses are known to affect natural rubber production. This study set out to identify abiotic stress-related miRNAs in Hevea using next-generation sequencing and bioinformatic analysis.

Results: 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 Hevea 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 MIR 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.

Conclusions: 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 Hevea.

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Pie chart representation of Gene Ontology terms at level 2 for putative targets of conserved (A and B) and novel miRNAs (C and D). A and C) Gene Ontology terms for biological processes, B and D) Gene Ontology terms for molecular functions.
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Figure 7: Pie chart representation of Gene Ontology terms at level 2 for putative targets of conserved (A and B) and novel miRNAs (C and D). A and C) Gene Ontology terms for biological processes, B and D) Gene Ontology terms for molecular functions.

Mentions: Computational prediction of miRNA targets led to the identification of 1,083 sequences for the 48 conserved families and 705 for the 10 putative novel miRNA families. Their involvement in biological processes and their molecular functions were attributed using Gene Ontology (Figure 7A, B, C and 7D). Most of the GO terms were represented in the same proportions for predicted targets from conserved and putative novel miRNA families. Target genes of the putative novel miRNA families all had GO terms of conserved miRNA families for biological processes and molecular functions. In biological process terms, the putative novel miRNA families had two additional terms (growth, cell wall organization or biogenesis). The number of miRNA target genes was smaller for putative novel than for conserved miRNAs for some GO terms: cellular process (25% as opposed to 27%), metabolic process (22% as opposed to 27%) and biological regulation (10% as opposed to 12%) (Figures 7A and 7C). This number was larger for putative novel miRNA targets compared to conserved targets for cellular component organization (5% as opposed to 3%), localization (7% as opposed to 4%) and response to stimulus (10% as opposed to 8%) (Figures 7A, B, C and 7D). As regards the GO terms for molecular function, although the distribution for antioxidant activity was the same for the 2 classes of miRNAs (1%), a decrease in the proportion of transcription regulator activity (4% as opposed to 7%) and an increase in structural molecule activity (4% as opposed to 2%) and transporter activity (7% as opposed to 4%) were observed for the putative novel miRNA families (Figures 7B and 7D).


Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets.

Gébelin V, Argout X, Engchuan W, Pitollat B, Duan C, Montoro P, Leclercq J - BMC Plant Biol. (2012)

Pie chart representation of Gene Ontology terms at level 2 for putative targets of conserved (A and B) and novel miRNAs (C and D). A and C) Gene Ontology terms for biological processes, B and D) Gene Ontology terms for molecular functions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368772&req=5

Figure 7: Pie chart representation of Gene Ontology terms at level 2 for putative targets of conserved (A and B) and novel miRNAs (C and D). A and C) Gene Ontology terms for biological processes, B and D) Gene Ontology terms for molecular functions.
Mentions: Computational prediction of miRNA targets led to the identification of 1,083 sequences for the 48 conserved families and 705 for the 10 putative novel miRNA families. Their involvement in biological processes and their molecular functions were attributed using Gene Ontology (Figure 7A, B, C and 7D). Most of the GO terms were represented in the same proportions for predicted targets from conserved and putative novel miRNA families. Target genes of the putative novel miRNA families all had GO terms of conserved miRNA families for biological processes and molecular functions. In biological process terms, the putative novel miRNA families had two additional terms (growth, cell wall organization or biogenesis). The number of miRNA target genes was smaller for putative novel than for conserved miRNAs for some GO terms: cellular process (25% as opposed to 27%), metabolic process (22% as opposed to 27%) and biological regulation (10% as opposed to 12%) (Figures 7A and 7C). This number was larger for putative novel miRNA targets compared to conserved targets for cellular component organization (5% as opposed to 3%), localization (7% as opposed to 4%) and response to stimulus (10% as opposed to 8%) (Figures 7A, B, C and 7D). As regards the GO terms for molecular function, although the distribution for antioxidant activity was the same for the 2 classes of miRNAs (1%), a decrease in the proportion of transcription regulator activity (4% as opposed to 7%) and an increase in structural molecule activity (4% as opposed to 2%) and transporter activity (7% as opposed to 4%) were observed for the putative novel miRNA families (Figures 7B and 7D).

Bottom Line: The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families.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 Hevea.

View Article: PubMed Central - HTML - PubMed

Affiliation: CIRAD, UMR AGAP, F-34398 Montpellier, France.

ABSTRACT

Background: 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 Hevea brasiliensis, environmental and harvesting stresses are known to affect natural rubber production. This study set out to identify abiotic stress-related miRNAs in Hevea using next-generation sequencing and bioinformatic analysis.

Results: 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 Hevea 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 MIR 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.

Conclusions: 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 Hevea.

Show MeSH