Based on the annotation of unigenes, 118 MADS-box genes were also discovered (Additional file 4: Table S3), these including the sepal development related genes such as APETALA1 (AP1), CAULOFLOWER (CAL); petal development related genes DEFICIENS (DEF)and PISTILLATA (PI); the C/D/E class function genes AGAMOUS (AG), SEEDSTICK (STK) and FLORAL BINDING PROTEIN-LIKE (FBP-like) were also identified. TCP gene family play important role in the development of plants and can be divided into two classes: PCF class and TCP-C class (which involes the CYC/TB1 clade and CIN clade) (Howarth and Donoghue 2006; Navaud et al. 2007). The CYC/TB1 clade includes genes mainly involved in the development of axillary meristems and floral bilateral symmetry (Luo et al. 1996; Doebley et al. 1997). To determine the TCP gene family in C. faberi, we analyzed the transcriptome database generated by this study and found 35 unigenes annotated as TCP TFs, including 14 CIN-like genes, 20 PCF-like genes and 1 CYC/TB1-like genes. As shown in Additional file 5: Table S4, they showed homology with 13 Arabidopsis TCP genes.