Identification of miRNAs in sorghum by using bioinformatics approach

MicroRNAs (miRNAs) regulate gene expression mainly by post-transcriptional gene silencing (PTGS) and in some cases by transcriptional genes silencing (TGS). miRNAs play critical roles in developmental processes, nutrient homeostasis, abiotic stress and pathogen responses of plants. In contrast to th...

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Bibliographic Details
Published in:Plant signaling & behavior 2012-02, Vol.7 (2), p.246-259
Main Authors: Katiyar, Amit, Smita, Shuchi, Chinnusamy, Viswanathan, Pandey, Dev Mani, Bansal, Kailash
Format: Article
Language:English
Subjects:
Binding
Biology
Bioscience
Calcium
Cancer
Cell
Computational Biology - methods
Cycle
Databases, Factual
Expressed Sequence Tags
Genes, Plant
Landes
MicroRNAs
miRNA
miRNA cluster
Organogenesis
Proteins
Research Paper
RNA, Plant
sorghum
Sorghum - genetics
Sorghum - growth & development
target genes
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Summary:MicroRNAs (miRNAs) regulate gene expression mainly by post-transcriptional gene silencing (PTGS) and in some cases by transcriptional genes silencing (TGS). miRNAs play critical roles in developmental processes, nutrient homeostasis, abiotic stress and pathogen responses of plants. In contrast to the large number of miRNAs predicted in cereal model plant rice, only 148 miRNAs were predicted in sorghum till date (miRBase release 17). This suggested that miRNAs identified in sorghum is far from saturation. Hence, we developed a bioinformatics pipeline using an in-house PERL script and publicly available structure prediction tools to identify miRNAs and their target genes from publically available Expressed Sequence Tags (EST) and Genomic Survey Sequence (GSS). About 1,379 known and unique plant miRNAs from 33 different crops were used to predict new miRNAs in sorghum. We identified 31 new miRNAs belonging to 10 different miRNA families. We predicted 72 potential target genes for 31 miRNAs, and most of these target genes are predicted to be involved in plant growth and development. These newly identified miRNAs add to the growing database of miRNA and lay the foundation for further understanding of miRNA function in sorghum plant development.
ISSN:1559-2316
1559-2324
1559-2324
DOI:10.4161/psb.18914