New wheat microRNA using whole-genome sequence
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MicroRNAs are post-transcriptional regulators of gene expression, taking roles in a variety of fundamental biological processes. Hence, their identification, annotation and characterization are of great significance, especially in bread wheat, one of the main food sources for humans. The recent availability of 5× coverage Triticum aestivum L. whole-genome sequence provided us with the opportunity to perform a systematic prediction of a complete catalogue of wheat microRNAs. Using an in silico homology-based approach, stem-loop coding regions were derived from two assemblies, constructed from wheat 454 reads. To avoid the presence of pseudo-microRNAs in the final data set, transposable element related stem-loops were eliminated by repeat analysis. Overall, 52 putative wheat microRNAs were predicted, including seven, which have not been previously published. Moreover, with distinct analysis of the two different assemblies, both variety and representation of putative microRNA-coding stem-loops were found to be predominant in the intergenic regions. By searching available expressed sequences and small RNA library databases, expression evidence for 39 (out of 52) putative wheat microRNAs was provided. Expression of three of the predicted microRNAs (miR166, miR396 and miR528) was also comparatively quantified with real-time quantitative reverse transcription PCR. This is the first report on in silico prediction of a whole repertoire of bread wheat microRNAs, supported by the wet-lab validation.
KeywordsTriticum aestivum MicroRNA MicroRNA prediction Next-generation sequencing Real-time quantitative reverse transcription PCR
RNA-induced silencing complex
Support vector machine
Expressed sequence tag
Low copy number assembly
Triticeae repeat database
Orthologous group assembly
Orthologous group representatives
Minimal folding free energy
Miniature inverted terminal repeat element
Transposable element-related miRNA group
Gene expression omnibus
Terminal inverted repeat
Long terminal repeat
Small interfering RNA
The authors are grateful to Dr. Rachel Brenchley and her collegues (Centre for Genome Research, University of Liverpool, UK) for use of the 5× coverage wheat genome assemblies and the transcriptome assembly.
Conflict of interest
The authors declare that they have no conflict of interest.
Experiments comply with the current laws of the country in which they were performed.
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