Abstract: This study identified of Ginkgo biloba flower bud differentiation key genes，to reveal the main molecular mechanism of ginkgo flower bud differentiation regulation，and provide theoretical guidance for shortening the juvenile phase and breeding early flowering varieties. High-throughput sequencing technology was used to sequence the transcriptomes of three different stages of flower bud differentiation，and digital expression profiles were analyzed to screen ginkgo flowering regulatory related genes. Genes were verified by qPCR. A total of 27.52 Gb of raw data was generated by transcriptome sequencing，and the total number of unigenes annotated in the 8 functional databases（GO，COG，KEGG，KOG，NR，Pfam，Swiss-Prot，and eggNOG）was 35 179. The unigenes were classified into 55 GO categories and 126 metabolic pathways. Analysis of differentially expressed genes revealed that 2 253 genes were up-regulated and 2 032 genes were down-regulated during the flower bud undifferentiated stage vs. initial stage of flower bud differentiation. A total of 1 770 genes were up-regulated and 1 901 genes were down-regulated during the initial stage of flower bud differentiation vs. flower bud differentiation stage. The flower bud undifferentiated stage vs. flower bud differentiation stage，1 865 genes were up-regulated and 2 042 genes were down-regulated. A large number of genes related to flowering were discovered，involving five flowering regulatory pathways（Photocycle pathway，Vernalization pathway，Gibberellin pathway，Autonomous pathway，and Age pathway）. Six key genes，such as gene.Gb_17618（GI unigene），gene.Gb_19790（FT/TFL1 unigene），gene.Gb_16301（AG unigene），gene.Gb_28337（MADS-box unigene），gene.Gb_01884（SOC1 unigene），and gene.Gb_41704（CO unigene），were selected. Their RT-qPCR expression was consistent with that of the transcriptome.

Key words: Ginkgo biloba, transcriptome sequencing, flowering regulation, GI, FT/TFL1, SOC1