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Saussurea lappa (S. lappa) has been known to synthesize medicinally important, costunolide. Due to its immense therapeutic importance, understanding of regulatory mechanism associated with its biosynthesis is crucial. The identification of genes and transcription factors (TFs) in S. lappa, created a clear picture of costunolide biosynthesis pathways. Further to understand the regulation of costunolide biosynthesis by miRNAs, an integrated study of transcriptome, miRNAs, and degradome was performed. Identified candidate miRNAs and associated feed-forward loops (FFLs) illustrates their regulatory role in secondary metabolite biosynthesis. Small RNA and degradome sequencing were performed for leaf and root tissues to determine miRNAs-targets pairs. A total of 711 and 525 such targets were obtained for novel and known miRNAs respectively. This data was used to generate costunolide-specific miRNA-TF-gene interactome to perform systematic analyses through graph theoretical approach. Interestingly, miR171c.1 and sla-miR121 were identified as key regulators to connect and co-regulate both mevalonate and sesquiterpenoid pathways to bio-synthesize costunolide. Tissue-specific FFLs were identified to be involved in costunolide biosynthesis which further suggests the evolutionary co-relation of root-specific networks in synthesis of secondary metabolites in addition to leaf-specific networks. This integrative approach allowed us to determine candidate miRNAs and associated tissue-specific motifs involved in the diversification of secondary metabolites. MiRNAs identified in present study can provide alternatives for bioengineering tool to enhance the synthesis of costunolide and other secondary metabolites in S. lappa.
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•Total of 662 and 373 miRNAs were identified from smRNAome data of leaf and root tissues of S. lappa respectively.•miRNA-TF-gene interactomes were constructed by integrating 5 types of interaction pairs (miRNA-TF, miRNA-gene, TF-miRNA, TF-gene, and gene-gene).•Precisely, miR171c.1 and sla-miR121 were identified as key regulators of the sesquiterpenoid biosynthetic pathway.•Transcription factor families, such as E2F/DP, GATA, and GRAS, were found to be involved in costunolide biosynthesis and regulated by miR6109, sla-miR4, sla-miR170, sla-miR337, sla-miR432, sla-miR537, sla-miR587, etc.•Leaf-specific feed-forward loops were studied to identify the central miRNA (sla-miRNA624, sla-miRNA417) associated with costunolides and other secondary metabolites biosynthetic pathways.•Similarly, root-specific feed-forward loop suggested role of miR6109, sla-miR997, sla-miR994, sla-miR752, etc in regulating costunolide biosynthesis.