RNA-Seq Analysis Revealed Differential Gene Expression and Exon-Specific Effects Associated with the Mating Process in Honey Bee Queens

Mating in honeybees causes dramatic changes not only in its behavior and physiology but in genes’ transcriptional level. To determine the molecular mechanisms regulating post-mating behavioral changes, we examined gene expression modification and exon-specific expression of the virgin queen versus the queen injected with semen in hemocoel. The DESeq2 package of R was used to identify the Differentially Expressed Genes (DEGs). The DEGs were selected for functional enrichment analysis and Protein-Protein Interaction (PPI) network construction. We also performed differential exon usage analysis using the DEXseq R package. Results identified a significant expression (FDR< 0.05) of a total of 971 genes between two groups of insects. The mating process produced significant changes in the expression of cell surface receptor signaling pathway, innate immune response, extracellular region, proteinaceous extracellular matrix, nucleous, G-protein coupled receptor activity, heme binding, and transmembrane transporter activity genes. Protein-Protein Interaction (PPI) network shows that LOC552504 (titin-like) could be considered as a super-hub gene in the mating process of queens. In addition, we identified exons that were differentially expressed in two groups of honeybee queens. At 10% FDR, we found significant differential exon usage in 79 genes. Among them, GB55396 gene had the most differences in exon usage and could be the best candidate gene for mating and reproductive activation in queens.