The FPKM methods were used to analyze the gene expression in the two libraries: 123,128 and 125,862 unigenes were obtained in the flower buds and vegetative buds, of which 39,549 and 42,283 genes expressed specifically in the flower buds and vegetative buds, respectively (Fig. 5). To analyze different gene expression in the two libraries, 13,484 DEGs were identified using FPKM methods. Among them, 7683 were down-regulated and 5801 were up-regulated in the flower buds when compared to those in the vegetative buds, including 3430 and 6556 genes specifically enriched in flower and vegetative buds, respectively. To validate and annotate the assembled DEGs, the 13,484 DEGs were subjected to BLASTX comparisons (E-value ≤10−5) against GO, COG and KEGG database to identify putative functions of these unigenes. As a result, 5348 (39.7 %), 2829 (21.0 %) and 3927 (29.1 %) DEGs had homologous sequences in GO, COG and KEGG databases, respectively. In addition, 5348 DEGs were classified into 44 GO term annotations, including cellular component (1399), biological process (3921) and molecular function (7006), with multiple terms assigned to the same transcript (Fig. 6). A total of 2829 DEGs were classified into 23 functional COG categories (Fig. 7). “general function prediction only” (506) was the most, followed by “posttranslational modification, protein turnover, chaperones” (248) and “transcription” (222). To further understand the function in biological processes, 3927 DEGs were classified into 245 KEGG pathways. These results showed that most of the DEGs were involved in the “metabolic pathways”(300), “biosynthesis of secondary metabolites”(252), “microbial metabolism in diverse environment (142)” and “ribosome”(89) (Table 4). After transcriptome analysis, TFs involved in the floral differentiation were revealed and their expression levels in the flower and vegetative buds were calculated and compared using the FPKM method.Fig. 5The numbers of specific genes and shared genes between the flower and vegetative buds of C. faberi Fig. 6GO classification of DEGs Fig. 7COG annotations of DEGs. 2829 DEGs were aligned to the COG database and were functionally classified into at least 23 molecular families. The capital letters in x-axis indicates the COG categories as listed on the right of the histogram and the y-axis indicates the number of unigenes in the corresponding COG category