Comparative Transcriptome Analysis Reveals bmo-miR-6497-3p Regulate Circadian Clock Genes during the Embryonic Diapause Induction Process in Bivoltine Silkworm

SIMPLE SUMMARY: Diapause is a type of seasonal polyphenism and is induced by multiple cues, such as light and temperature. However, the molecular mechanisms of how the environment induces diapause remains unclear. We are interested in the epigenetic regulation, especially the non-coding RNA, involved in environmentally induced diapause. The progeny eggs of bivoltine silkworm strains undergoing diapause or not depends on the incubation temperature during the maternal embryonic stage. In this research, we compared the differentially expressed microRNAs in embryos incubated under diapause-inducing temperature (25 °C) and non-diapause-inducing temperature (15 °C) in silkworm. Our results indicate that miRNAs respond to diapause-inducing temperature and regulate the expression of circadian clock genes. Our research not only provides reference for the study of the diapause induction process, but also gives insights into the role of epigenetic modification in diapause. ABSTRACT: Diapause is one of the survival strategies of insects for confronting adverse environmental conditions. Bombyx mori displays typical embryonic diapause, and offspring diapause depends on the incubation environment of the maternal embryo in the bivoltine strains of the silkworm. However, the molecular mechanisms of the diapause induction process are still poorly understood. In this study, we compared the differentially expressed miRNAs (DEmiRs) in bivoltine silkworm embryos incubated at diapause- (25 °C) and non-diapause (15 °C)-inducing temperatures during the blastokinesis (BK) and head pigmentation (HP) phases using transcriptome sequencing. There were 411 known miRNAs and 71 novel miRNAs identified during the two phases. Among those miRNAs, there were 108 and 74 DEmiRs in the BK and HP groups, respectively. By the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the predicted target genes of the DEmiRs, we found that aside from metabolism, the targets were also enriched in phototransduction-fly and insect hormone biosynthesis in the BK group and the HP group, respectively. Dual luciferase reporter assay illustrated that bmo-miR-6497-3p directly regulated Bmcycle and subsequently regulated the expression of circadian genes. These results imply that microRNAs, as vitally important regulators, respond to different temperatures and participate in the diapause induction process across species.