Sex-specific mRNA and miRNA alterations in the allergic mite species <i>Dermatophagoides farinae</i>

miRNA-mRNA interactions regulate mite physiology and behavior, especially in response to growth- and reproduction-affecting environmental factors. Despite being a major source of allergens, gender-specific mRNA and miRNA expression in allergic mites has not yet been explored. Male and female Dermatophagoides farinae mites were manually selected under a stereomicroscope and used for library preparation for mRNA and small RNA sequencing, following standard Illumina protocols. Differential expressions of mRNA and miRNAs were analyzed separately and validated by qRT-PCR. An mRNA-miRNA regulatory network was then constructed using computational target prediction algorithms, with further validation through a dual-luciferase reporter assay. Compared to female mites, male mites exhibited 321 upregulated and 430 downregulated genes. GO analysis revealed significant differences in gene sets associated with DNA replication, RNA polymerase complexes, and sex differentiation between the two sexes. A total of 130 miRNAs showed differential expression, with 51 miRNAs upregulated in male mites. Integrated analysis of mRNA and miRNA sequencing data predicted 29 specific miRNAs targeting distinct mRNAs, with key genes and miRNAs further validated by qRT-PCR. Additionally, dual-luciferase reporter assays confirmed that PC-5p-65423_75 regulates the developmental processes of male and female mites by targeting Sex Comb on Midleg Like-2 (SCML2). This study provides a comprehensive analysis of the transcriptome and small RNA sequencing of D. farinae. We identified key miRNAs and their target genes, offering valuable insights into the reproductive and growth strategies of allergic mites.