Azadirachta indica MicroRNAs: Genome-Wide Identification, Target Transcript Prediction, and Expression Analyses

Area of Science:

• Plant molecular biology
• Genomics
• Biotechnology

Background:

• MicroRNAs (miRNAs) are crucial endogenous non-coding RNAs regulating gene expression in plants.
• While many plant miRNAs are known, none have been identified in the medicinal tree Azadirachta indica (Neem).
• Genomic and transcriptomic resources for Neem exist, but miRNA discovery is lacking.

Purpose of the Study:

• To identify microRNAs (miRNAs) and predict their targets in Azadirachta indica (Neem) for the first time.
• To explore the potential therapeutic roles of Neem miRNAs.
• To understand the regulatory functions of identified miRNAs in plant processes.

Main Methods:

• Genome-wide identification of miRNAs in Azadirachta indica using the C-mii tool.
• Prediction of miRNA stem-loop hairpin structures and precursor sequences.
• Target gene prediction in both Azadirachta indica and Arabidopsis thaliana.
• Gene Ontology (GO) annotation of target genes.
• Stem-loop quantitative reverse transcription PCR (qRT-PCR) for expression analysis.

Main Results:

• 123 microRNAs (miRNAs), categorized into 63 families, were identified in Azadirachta indica.
• Predicted miRNAs range from 19-23 nucleotides, with an average precursor MFEI of -1.147 kcal/mol.
• Target genes are involved in developmental, transport, stress, and metabolic processes, including secondary metabolism.
• Differential expression patterns of 25 selected miRNAs were observed across different Neem tissues.
• A negative correlation was found between miRNA and target gene expression.

Conclusions:

• This study provides the first comprehensive identification of microRNAs (miRNAs) in Azadirachta indica (Neem).
• Identified miRNAs and their targets are implicated in essential plant functions, suggesting therapeutic potential.
• The findings lay the groundwork for understanding miRNA-mediated regulation in Neem and its medicinal applications.