| The honey bee (Apis mellifera) is a highly diverse species commonly used for honey production and pollination services. Oviposition of honey bee queen affects the development and overall performance of the colony. To analyze the differentially expressed coding and noncoding RNAs in the processes of ovary activation and oviposition regulation, and further identify candidate genes and/or RNAs for oviposition, a genome-wide analysis of IncRNAs, mRNAs, miRNA and circRNAs expression in queens’ ovaries was performed.In this study, we examined the lncRNA, mRNA, miRNA and circRNA expression profiles in ovaries of virgin queens (n=3), egg-laying queens (n=3),egg-laying inhibited queens (n=3) and egg-laying recovered queens (n=3)using high throughput sequencing. The analysis revealed that 224 IncRNAs,3218 mRNAs, 39 miRNAs and 228 circRNAs were up-regulated and 516 IncRNAs, 2263 mRNAs, 42 miRNAs and 272 circRNAs were down-regulated during the queens’ ovary activation. During the queens’oviposition inhition process, 57 IncRNAs, 266 mRNAs, 9 miRNAs and 273 circRNAs were up-regulated and 31 lncRNAs, 72 mRNAs, 4 miRNAs and 227 circRNAs were down-regulated. During the queens’ oviposition recovery process, 40 IncRNAs, 256 mRNAs, 2 miRNAs and 236 circRNAs were up-regulated and 60 IncRNAs, 241 mRNAs, 2 miRNAs and 264 circRNAs were down-regulated. All these differentially expressed RNAs were functionally annotated in order to identify biological processes and genetic pathways overrepresented. Several biological processes, including system development, biological regulation and neuron differentiation, were enriched with the differentially expressed RNAs. Further, several pathways were found closely related to oviposition, including Wnt, hippo, TGF-beta, notch, MAPK,FoxO and mTOR signaling pathways.In the QTL region for ovary size, 73 differentially expressed genes and 14 differentially expressed IncRNAs were located, which are considered as candidate genes affecting ovary size and oviposition.Analysis of gene-act-network of target genes of DE circRNAs revealed the key roles in the network: ECR、E75、E74、IR-B and RACK1. Moreover, a core set of genes served as "bridges" among different miRNAs were identified through the integrated analysis of IncRNA-miRNA-mRNA and circRNA-miRNA-mRNA network. Key roles in the network, CCDC93 and Hsc70-3, were discussed.The dramatic expression changes of coding and noncoding RNAs were observed in this study, which suggested that they could play a critical role in honey bee queens’ oviposition. Moreover, candidate genes for oviposition activation and regulation were identified, and could serve as a resource for further studies of genetic markers of oviposition in honey bees. |
