Catharanthus roseus, produces a diverse array of specialized metabolites known as monoterpene indole alkaloids (MIAs) through an extensive and intricately branched metabolic pathway. It is imperative to unravel the intricate regulatory networks and relationships between the genes involved in the production of these metabolites. Long non-coding RNAs (lncRNAs) are emerging as significant regulatory factors in various biological processes. In this study, 4303 out of 86726 transcripts were identified as potential lncRNAs in C. roseus. Subsequently, we identified coding genes that exhibited a high correlation with CrlncRNA, designating them as potential target genes for collectively modulating the MIA pathway using Weighted Gene Co- Expression Network Analysis (WGCNA), leading to the identification of crucial gene clusters associated with the biosynthesis of MIAs. Based on the findings, three modules (dark turquoise, magenta, and orange) and hub genes were pinpointed as being linked to MIAs. Additionally, the most prominent known coding genes were 10- hydroxygeraniol oxidoreductase, GATA-like transcription factor (GATA1), 7- deoxyloganetic acid UDP-glucosyltransferase (7DLGT), desacetoxyvindoline 4- hydroxylase (DH4), MYC2, and MPK6. The unknown target genes were related to stress response and the intricate process of hormone transduction. ORCA, MYC2, and GATA1 are crucial in regulating the MIA pathway, likely requiring cooperation with CrlncRNAs.

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