Fazaneh Aram - Institute of Biotechnology, Shiraz University, Shiraz, Iran.
Seyed Hassan Marashi - Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
Ahmad Tahmasebi - Institute of Biotechnology, Shiraz University, Shiraz, Iran.
Alireza Seifi - Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
Behzad Shahin Kaleybar - Department of Plant Breeding and Biotechnology, SANRU, Sari, Iran.

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, ۴۳۰۳ out of ۸۶۷۲۶ 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 ۱۰-hydroxygeraniol oxidoreductase, GATA-like transcription factor (GATA۱), ۷-deoxyloganetic acid UDP-glucosyltransferase (۷DLGT), desacetoxyvindoline ۴-hydroxylase (DH۴), MYC۲, and MPK۶. The unknown target genes were related to stress response and the intricate process of hormone transduction. ORCA, MYC۲, and GATA۱ are crucial in regulating the MIA pathway, likely requiring cooperation with CrlncRNAs.

lncRNAs, Specialized metabolites, Transcription factors (TFs), Medicinal plants, Gene Modules