Honeybees are vital pollinators with functional differentiation as a key survival strategy. The Chinese honeybee (Apis cerana cerana) exhibits exceptional nectar foraging in complex terrains, yet how alternative splicing (AS) and polyadenylation (APA) regulate its labor division remains unclear. Here, we applied PacBio full-length transcriptome sequencing to annotate worker bee transcriptomes across three developmental stages (Ac3d, Ac10d, Ac21d), calibrating the third-generation sequencing data with second-generation sequencing to enhance transcriptome annotation accuracy. We identified 17,961 isoforms and 1922 APA genes, finding that alternative first exon was the major type of AS, while APA enhances transcriptomic diversity via dual polyadenylation sites in most genes. Functional analyses revealed AS enrichment in growth signaling (Vg6, CYP15A1) and immune pathways (PTPRR), whereas APA regulated growth signaling (Vg6), energy metabolism (Acsl1, AcceFE), and oxidative stress (PTPRR, PPO2). Validation by PCR and 3′RACE confirmed stage-specific AS/APA events in key genes. These findings significantly enhance the A. cerana cerana reference genome annotation and provide valuable insights into the mechanisms of AS and APA regulation underlying honeybee development and functional transitions.

Honeybees are important pollinators that enhance food safety and promote biodiversity. However, honeybees are increasingly threatened by insecticide use. Matrine, a plant-derived insecticide, has been used in plants, such as pear trees, citrus, and cotton whose flowers are a honey source. Despite matrine’s economic significance, its impact on bees is rarely reported. In this study, honeybees (Apis cerana) were exposed to three concentrations (1.2, 10, and 40 mg/L) of matrine. Continuous matrine intake caused rapid death of honeybees on day 9 but had no significant effect on food consumption and body weight of the honeybees. Matrine intake caused changes in the abundance of Gilliamella, Dorea, and Lachnoclostridium in gut microbiota, resulting in the differential expression of argininosuccinic acid, spermidine, arachidonic acid, and LOC107998471 (Aldh). This finding underscored the role of these microbiotas, metabolites, and genes in honeybees under matrine stress. This study provides a comprehensive explanation of matrine toxicity to honeybees and reveals the crucial microbiota, metabolites, and genes. These findings provide important references for honeybee poisoning and the associated detoxification mechanism.