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Updated: Oct 10, 2026
Embryo Microinjection and Knockout Mutant Identification of CRISPR/Cas9 Genome-Edited Helicoverpa Armigera (Hübner)
Published on: July 1, 2021
Transcriptome profiling across fifteen cotton pests unveils inter and intra-order gene biomarkers for targeted pest
Julie Rebecca Joseph Mathari1, Habeeb Shaik Mohideen1
1Bioinformatics and Integrative Omics lab, Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, 603203 Tamil Nadu India.
Abstract:
Cotton cultivation faces severe challenges by diverse biotic stresses, such as pests, leading to substantial yield losses and increased production costs. Comparative transcriptomic analyses across multiple cotton pests and orders remain largely unexplored, restricting the identification of conserved broad-spectrum molecular targets for sustainable pest management. This study uncovers transcriptome dynamics across fifteen economically important cotton pest species representing four insect orders (Hemiptera, Lepidoptera, Orthoptera, and Thysanoptera) to identify inter-species and inter-order differential gene expression patterns and potential candidate biomarkers. Comparative differential expression analysis revealed distinct lineage-specific profiles, with Nezara viridula exhibiting pronounced downregulation with 1141 downregulated genes, while Helicoverpa armigera exhibited the highest gene expression with 1816 upregulated genes. Order-level clustering highlighted marked transcriptomic divergence within Lepidoptera, contrasting with a tightly unified profile in Hemiptera. Functional annotation identified conserved differential expression of genes associated with reproduction, protein regulation, and stress responses. Core reproductive and development-related genes such as vitellogenin and translationally controlled tumour protein (TCTP) were consistently downregulated across Hemiptera, Lepidoptera, and Orthoptera, whereas Ras, Peptidase, and ThiF gene families were predominantly upregulated in Hemiptera and Lepidoptera. Pathway enrichment analysis reinforced these trends showing biological processes associated with amino acid metabolism, protein processing, and cellular regulation. These findings provide a comprehensive comparative transcriptomic resource for cotton pests and identify conserved candidate hub genes and pathways that may facilitate the development of RNA interference-based and other sustainable integrated pest management strategies.
Supplementary Information:
The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05051-z.
