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MicroRNAs are small sized endogenous non-coding RNA, of ~18‐25 (nt) that regulates the expression of their target genes in plants at post transcriptional level and play very significant roles in multiple biological processes. These ribosw itches may play the role of master regulator in important biological processes and plant metabolic pathways. In the present study, we performed small RNA profiling to identify miRNAs present in the holy tree Aegle marmelos and their involvement in different metabolic pathways. A total of 9,192,725 (88.52%) clean reads out of 10,384,409 (100%) reads were identified with size ranging from 15‐ to 24 nt. Using computational tools and bioinformatics approaches we revealed around 253 conserved miRNAs accounting into 20 miRNA families and a total of 395 annotated targets were found for 6 novel miRNAs within the plant. Functional annotation revealed Homeobox-leucine zipper protein and ERF like transcription factors as targets of conserved miRNAs. The present study provides a first report on elucidation of genome-wide miRNA profile of A. marmelos which can be further explored to manipulate their expression to scale-up biosynthesis of active metabolites using metabolic engineering approaches.

Aegle marmelos (L.) also known as Bael is a medicinally important tree known for its antidiabetic properties. It is considered as a sacred plant but lacks sufficient genomic and transcriptomic resources. The present study investigated functional profile of A. marmelos via RNA sequencing technology. The denovo transcriptome sequencing and assembly of 4.7 million high quality reads yielded 27,393 unigenes, which were annotated against the databases such as NCBI (National Centre for Biotechnology Information), NR (Non redundant) database, KEGG, Pfam (Protein Family), CDD (Conserved Domains database) and Uniprot. The annotation of assembled transcripts showed a total of 1291 transcripts mapped to 81 different transcription factor families, whereas 55 transcripts were assigned to CYP450 belonging to 21 different classes. KEGG mapping showed transcripts involved in the biosynthesis of terpenoids, flavonoids, including transcripts for synthesis of important compounds like Vitamin E, 4-coumarate and Vitamin K epoxide. 1211 simple sequence repeats (SSRs) were identified which may aid in molecular breeding studies. The study provides an insight into the expression profile of Bael and an opportunity for future genomic and metabolic studies in A.marmelos.