Comparing of transcriptome profiles between queen- and worker-destined larvae in honey bee by RNA-Seq

Caste differentiation in female honey bee is one of the most intriguing polyphenism phenomena. This developmental switch depends not on genomic differences between queens and workers but on the differential expression of entire suites of genes involved in larval fate. In this study, we compared transcriptome differences between full-sister queen- (QL) and worker-destined larvae (WL) by high-throughput RNA-Seq. Consequently, four libraries prepared from QL and WL at fourth- (L4) and fifth-instar (L5) generated 50,191,699 (QL4), 57,628,541 (WL4), 56,613,619 (QL5), and 58,626,829 (WL5) usable reads, which were assembled into 7,952, 7,993, 7,971, and 8,023 genes, respectively. Transcriptome changes were investigated using DEGs Package (DEGseq) which resulted in more than 4,500 Differentially Expressed Genes (DEGs) between castes. Eight of them were verified by quantitative real-time RT-PCR, and results supported our sequencing data. All DEGs were analyzed using WEGO and then mapped to KEGG. Results suggested that: 1) more than 70% DEGs were highly expressed in QL than in WL in each instar, possibly reflecting that genes of QL had higher transcriptional activity than paralleled WL during differentiation; 2) QL and WL respectively own a special set of active genes to fulfill similar functions; 3) The important period to complete development and/or differentiation is L4 for both QL and WL before their pupal stage; 4) Activity of mTOR (target of rapamycin) encoding gene in mTOR signaling pathway is elevated in QL4 than WL4, while this different was no longer present in L5 (feeding stage). Genes down-stream of mTOR kept this change in L5. These results could contribute to the in-depth study of candidate genes during caste differentiation in honey bee, and help improve current understanding of polyphenism phenomenon in insects.