Genome-wide identification, expression and functional analysis of the core cell cycle gene family during the early somatic embryogenesis of Dimocarpus longan Lour

•A total of 69 core cell cycle genes (CCCs) family members were identified in the longan genome.•Either silencing of CKS or CYCD3;2 increased the expression of RB-E2F pathway-related genes.•Silencing of CYCD3;2 might lead to apoptosis in longan embryogenic callus.•ABA, 2,4-D and PEG4000 could increase the expression of all selected longan CCCs, while NaCl did not. Core cell cycle genes (CCCs) are essential regulators of cell cycle operation. In this study, a total of 69 CCCs family members, including 37 CYCs, 20 CDKs, five E2F/DPs, three KRPs, two RBs, one CKS and one Wee1, were identified from the longan genome. Phylogenetic and motifs analysis showed the evolutionary conservation of CCCs. Transcriptome dataset showed that CCCs had various expression patterns during longan early somatic embryogenesis (SE). Either CKS or CYCD3;2 silencing increased the expression of RB-E2F pathway genes, and the silencing of CYCD3;2 might induce the process of apoptosis in longan embryogenic callus (EC) cells. In addition, The qRT-PCR results showed that the expression levels of CDKG2, CYCD3;2, CYCT1;2, CKS and KRP1 were elevated by ABA, 2,4-D and PEG4000 treatments, while CDKG2 and CYCT1;2 were inhibited by NaCl treatment. In conclusion, our study provided valuable information for understanding the characterization and biological functions of longan CCCs.