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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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Length distribution of reads matching miRNA families in Hevea brasiliensis. (A) conserved miRNA (B) putatively novel families.
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Figure 2: Length distribution of reads matching miRNA families in Hevea brasiliensis. (A) conserved miRNA (B) putatively novel families.

Mentions: Reads of conserved and putative novel miRNAs were distributed according to their nucleotide lengths (Figure 2). The 48 conserved miRNA families mostly had 24 and 23 nucleotides (Figure 2A). For the 10 putative novel miRNA families, the most represented lengths were 24, 27 and 26 nucleotides (Figure 2B).


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)

Length distribution of reads matching miRNA families in Hevea brasiliensis. (A) conserved miRNA (B) putatively novel families.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Length distribution of reads matching miRNA families in Hevea brasiliensis. (A) conserved miRNA (B) putatively novel families.
Mentions: Reads of conserved and putative novel miRNAs were distributed according to their nucleotide lengths (Figure 2). The 48 conserved miRNA families mostly had 24 and 23 nucleotides (Figure 2A). For the 10 putative novel miRNA families, the most represented lengths were 24, 27 and 26 nucleotides (Figure 2B).

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