Cry2 linked silkworm domestication to highly synchronized eclosion and rhythmic head transcriptomes

Domestication often enhances the temporal synchronization of life-history events; yet the underlying molecular mechanisms remain poorly understood. Here, we investigated the circadian basis of domestication-associated synchronization by comparing eclosion rhythms and circadian transcriptomes between the domesticated silkworm ( Bombyx mori ) and its wild ancestor ( B. mandarina ), and functionally dissected the role of the clock gene Cry2 . Under 14:10 light–dark cycles, both species exhibited significant daily eclosion rhythms; however, B. mori showed markedly higher synchronization and a distinct phase advance, resulting in a sharply clustered early-morning peak compared with the broader afternoon pattern in B. mandarina . Cry2 knockout did not substantially affect eclosion timing under LD cycles, but under constant darkness it delayed phase, reduced robustness and synchronization of the eclosion rhythm, suggesting that Cry2 promotes the precision and synchrony of endogenous eclosion rhythms. To uncover transcriptional signatures of domestication, we performed 24-h RNA-seq on heads of domestic, wild, and Cry2 -mutant silkworms. Thousands of rhythmic genes and broad oscillatory expression of core clock genes were detected in B. mori , whereas only dozens of rhythmic transcripts were found in B. mandarina . Disruption of Cry2 strongly reduced the detectable domestication-expanded rhythmic transcriptional program, reducing the number of rhythmic genes from thousands to fewer than one hundred. Rhythmic outputs in B. mori were enriched in protein processing in the endoplasmic reticulum, Toll/Imd signaling, and daytime-biased tyrosine metabolism/dopamine biosynthesis pathways. Co-expression network analysis further revealed that domestication strengthened clock-linked regulatory networks, which became fragmented in both the Cry2 mutant and wild silkworms. These findings demonstrate that domestication promotes interindividual synchronization of eclosion by expanding and coordinating circadian transcriptional programs, suggesting that Cry2 acts as a potential candidate gene contributing to this adaptive rhythmic network.