Multi-omics analysis reveals the ontogenesis of basal chichi in Ginkgo biloba L

Chichi is a unique biological phenomenon observed in Ginkgo biloba L.. In this study, multi-omics analysis was used to compare basal chichi (C) with roots (R) and stems (S) to explore the regulatory mechanisms of basal chichi ontogenesis. The results showed that compared with roots and stems, the tZ, SA and ABA contents in basal chichi were the highest, and the ratio of IAA/tZ was the lowest. Nucleotides and their derivatives in basal chichi were upregulated, and phenylpropane metabolites were downregulated. Some differentially expressed genes (DEGs) strongly correlated to plant hormones were screened. We speculate that auxin and cytokinin are involved in the morphogenesis of basal chichi and that cytokinin plays a major role. The ontogenesis of basal chichi is closely related to environmental stress, and it may be a coping strategy of G. biloba in the face of environmental stress. •RNA-seq and LC-MS/MS were used to explore the ontogenesis mechanism of basal chichi.•Cytokinin plays a major role in the morphogenesis of Ginkgo biloba basal chichi.•Basal chichi may be a coping strategy of G. biloba in the face of environmental stress.