The mitochondrial genome provides crucial information for understanding the evolution and phylogeny of various Apis cerana populations. Apis cerana -Southern China is a unique ecological type of Asian bee, A. cerana , primarily found in the coastal mountains of South China. Here, we used PacBio-HiFi sequencing to obtain the complete mitochondrial genome of A. cerana -Southern China and infer the phylogenetic relationships between A. cerana -Southern China and other A. cerana ecotypes. The mitochondrial genome of A. cerana -Southern China contains 16,137 bp and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and an AT-rich region. The overall base composition is as follows: A (42.41%), C (9.59%), G (6.18%), and T (41.82%). The combined percentage of A and T (84.23%) is significantly higher than that of G and C. Among the 37 genes, 23 were located on the majority strand, while the remaining 14 were located on the minority strand. The phylogenetic tree based on the 13 PCGs showed that the genetic distance between A. cerana -Southern China, A. cerana -Central China, and A. cerana -Aba was closer. The complete mitochondrial genome sequence reported here would be useful for further phylogenetic analysis and conservation genetic studies in A. cerana -Southern China.

Background/Objectives: The larval stage plays a pivotal role in determining caste and sex in Apis mellifera. This study integrates RNA-seq, WGCNA, and alternative splicing analyses to explore gene expression differences among 2-day-old worker, drone, and queen larvae. Methods: RNA-seq was conducted on 2-day-old larvae from all three castes. Differential expression, WGCNA, and alternative splicing patterns were investigated. A deep learning TCN model was trained using WGCNA-derived modules and demonstrated high classification accuracy. Results: The TCN model highlighted a top-10 gene set, including PDHB, Fibroin3, and LOC724161. Significant caste- and sex-specific splicing events were detected in Tk, Csd, and Fem, with AF events being most prevalent. Splicing differences between sexes exceeded those observed among castes. Conclusions: The 2-day-old larval stage is crucial for both caste and sex differentiation in honeybees. This study identifies key genes and splicing events, offering new insights into the molecular mechanisms underlying caste formation and sex determination.

Background/Objectives: Early larval development is critical for caste and sex differentiation in honeybees. This study investigates molecular divergence in 4-day-old Apis mellifera larvae and introduces a customized deep learning model for hub-gene discovery. Methods: Genome-guided RNA-seq, DEGs, WGCNA, and splicing analyses were integrated. A hybrid convolution–attention model, ACmix-Swin, combined with WGAN-GP augmentation, was developed to classify larvae and prioritize caste-biased genes. Selected genes were validated by qPCR. Results: Significant caste- and sex-specific divergence was detected in cuticle formation, hormone metabolism, and reproductive signaling. ACmix-Swin achieved the highest accuracy among baseline models and consistently identified key regulators, including Vg, LOC725841, LOC412768, and LOC100576841. qPCR confirmed RNA-seq trends. Conclusions: Caste- and sex-specific transcriptional programs are established early in larval development. The ACmix-Swin framework provides an effective strategy for high-dimensional transcriptome interpretation and robust hub-gene identification.