De Novo transcriptome assembly of Diaprepes abbreviatus: foundations for functional genomics and targeted pest management

BACKGROUND: Diaprepes abbreviatus is a major pest causing severe root damage and yield loss in over 150 species, with a complex life cycle that hinders effective control. Limited genomic and transcriptomic resources have restricted molecular insights into its biology. De novo transcriptome assembly provides a practical approach for reconstructing the full set of transcripts in organisms without a reference genome, enabling the identification of novel genes and isoforms as well as the study of gene expression patterns. RESULTS: We performed RNA-seq across seven developmental stages of D. abbreviatus, generating a high-quality de novo transcriptome assembly comprising 991,860 unique transcripts and 505,007 unigenes with 99.2% completeness based on BUSCO analysis. Gene structure annotation predicted 75,895 coding sequences with an average length of 1,079 bp. Comparative transcriptomic analysis of adult males and females identified 16,082 significantly differentially expressed transcripts, emphasizing distinct sex-biased gene expression patterns. Functional classification revealed major enrichment in metabolism, signal transduction, transport, and developmental processes. Additionally, genes related to mitochondrial function, muscle structure, and detoxification pathways exhibited clear sex-specific expression. Gene Ontology (GO) and KEGG pathway analyses further emphasized enrichment in detoxification, xenobiotic metabolism, and hormonal regulation pathways. We further validated this differential expression data by RT-qPCR analysis. CONCLUSIONS: We present a high-quality de novo transcriptome assembly of D. abbreviatus with detailed, stage-specific transcript coverage. The identification of key developmentally regulated genes offers valuable insights into the molecular mechanisms underlying their biology. This resource lays the groundwork for future functional studies and the development of targeted pest management strategies, contributing to sustainable control of this economically important pest. SUPPLEMENTARYY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-11880-8.