Transcriptome profiling to decipher molecular mechanisms of diapause in Chilo partellus (Swinhoe) (Lepidoptera:...

Diapause is a critical adaptive strategy in insects to survive unfavourable environmental conditions. The present study investigated molecular mechanisms underlying diapause in Chilo partellus, using high-throughput RNA sequencing and de novo transcriptome assembly. Six transcriptome libraries from diapause and non-diapause larvae yielded over 50 million reads per sample, with >98% mapping efficiency. The Evidential Gene-refined assembly produced 67,116 high-quality transcripts, and BUSCO analysis confirmed its completeness. DEG analysis identified 1204 DEGs, including 660 upregulated and 544 downregulated in diapause larvae. GO enrichment revealed significant activation of stress response pathways, including heat shock proteins, protein folding, and redox homeostasis. Hormone-related genes such as juvenile hormone epoxide hydrolase and juvenile hormone esterase-like transcripts that are associated primarily with hormone degradation or early steps of ecdysteroidogenesis rather than direct synthesis of active ecdysteroids, were upregulated, suggesting endocrine regulation of diapause. Conversely, downregulation of insulin-like peptides, mitochondrial respiratory genes, and ribosomal proteins reflected suppressed metabolic and translational activity, hallmarks of diapause. PCA and hierarchical clustering confirmed clear transcriptional separation between diapause and non-diapause stages. Ten representative DEGs were validated using qRT-PCR, demonstrating strong concordance with RNA-seq. Notably, upregulated genes included Hsp70-like proteins, cytochrome P450s, and cuticle proteins, while insulin signaling and oxidative phosphorylation were downregulated. This study provides a comprehensive molecular framework for diapause in C. partellus, highlighting stress tolerance, metabolic suppression, and hormonal control as key regulatory themes. The identified genes offer potential targets for disrupting diapause, contributing to improved pest management strategies against this economically important insect.