Isoform-resolved transcriptomics reveals stage-specific isoform switching and protein domain remodeling in Helicoverpa armigera

Insects exhibit pronounced developmental plasticity, driven by complex regulation of gene expression, including isoform-level modulation across developmental stages. However, the role of isoform-level regulation in the developmental transitions of Helicoverpa armigera remains underexplored. Here, we performed transcriptome analysis to characterize gene isoform–specific expression changes between the pupa and adult stages of H. armigera. Differential gene-isoform expression analysis revealed that many multi-isoform genes displayed distinct stage-biased regulation that was undetectable at the gene level, uncovering hidden layers of transcriptional complexity. Functional enrichment analyses of differentially expressed multi-isoform genes highlighted MAPK, Hippo, Wnt and apoptosis pathways, consistent with major cellular remodeling processes during the pupa to adult transition. Isoform switching analysis further identified isoform usage shifts between stages, particularly among genes associated with signaling and metabolic regulation. Protein domain and structural modeling revealed that several isoform pairs differed in domain composition, sequence identity, and predicted fold conformation, indicating potential functional divergence in isoform switched genes. Together, these findings suggest that isoform-level modulation may contribute to stage-specific diversification in H. armigera. This work establishes a foundation for understanding isoform‑driven developmental plasticity in insects and underscores the importance of isoform-level resolution for elucidating mechanisms of developmental gene regulation.