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

BMC Plant Biology
Virginie GébelinJulie Leclercq

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 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. 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 miR...Continue Reading

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Citations

Dec 26, 2012·Antioxidants & Redox Signaling·Sabine LüthjeKerstin Wöltje
Jan 18, 2013·BMC Genomics·Cuifang DuanPascal Montoro
Feb 5, 2013·BMC Genomics·Ahmad Yamin Abdul RahmanMaqsudul Alam
Oct 3, 2013·International Journal of Molecular Sciences·Virginie GébelinPascal Montoro
Jun 29, 2014·Journal of Plant Physiology·Manassawe LertpanyasampathaJarunya Narangajavana
May 27, 2014·Molecular Genetics and Genomics : MGG·Supanath KanjanawattanawongJarunya Narangajavana
Mar 1, 2014·Applied Biochemistry and Biotechnology·Xi Hong SunZhan Bin Wang
Apr 17, 2018·Non-coding RNA·Kavitha Velayudha Vimala KumarGopal Pandi
Nov 28, 2018·Molecular Genetics and Genomics : MGG·Mingqin Zhou, Wei Tang
Feb 2, 2021·Applied Biochemistry and Biotechnology·Raja RajakaniVikrant Gupta

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Methods Mentioned

BETA
electrophoresis
454 sequencing
PCR
Illumina sequencing

Software Mentioned

Gene
BLASTN
LeARN
_ Adaptor
lmiRNA
Miranda
Blast2GO
Sun Grid Engine
WU nrdb
psRNAtarget server

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