Auxin and cytokinin mediated regulation involved in vitro organogenesis of papaya

•We report an efficient protocol for papaya callus induction and shoot regeneration.•Auxin and cytokinin pathway genes are involved in papaya in vitro organogenesis.•Identified two key transcription factors CpLBD19 and CpESR1 may regulate callus and shoot formation of papaya.•A gene regulatory network model of papaya in vitro organogenesis is presented.