Mol Genet Genomics(2015)290:239-255 245 E (SEP1/2/3) AGL6 A (AP1/FU儿U CAL) AGL12 -030 MIKC 014 C/D BrMAD (AG/ STK/ SHP1/2) FLC MAF TM3-like (S0C1) (AP3/PD Bs Arabidopsis type ll MADS-box genes (TT16) ◆ Rice type ll AGL17 MADS-box genes AGL18/15 SVP Fig.2 Phylogenetic tree of Chinese cabbage,Arabidopsis and rice rice (41)showing similar groups in all of the plant species.In total type II MADS-box proteins.Phylogenetic analysis of 182 type II 13 clades with different colours that were formed by type II MADS MADS proteins from Chinese cabbage (95),Arabidopsis (46)and proteins are also marked (colour figure online) the gene number in the Chinese cabbage genome was nota- the correlation of the MADS-box genes in Chinese cabbage bly less than three times the Arabidopsis gene number and Arabidopsis,the networks of MADS-box genes were because some genes were lost during polyploidy speciation. constructed using these two species orthologous (Sup- Additionally,both segmental and tandem gene duplications plementary Fig.7).Among the orthologous gene pairs of have significant impacts on the expansion and evolution of Chinese cabbage and Arabidopsis,16 Arabidopsis MADS- gene families in plant genomes.In this study,we analysed box genes were found no ortholog with Chinese cabbage the ortholog groups between Chinese cabbage and Arabi- MADS-box genes,these genes have been duplicated in dopsis MADS-box genes using the OrthoMCL program. Arabidopsis after the split.Fifty Arabidopsis MADS-box Then,we identified 67 orthologous gene pairs and 120 co- genes have only one ortholog in Chinese cabbage,these orthologous gene pairs in the MADS proteins of these two genes were present before the split,but two of the three species (Supplementary Table 6).Their visualisation was copies have been lost after the B.rapa genome triplica- performed using the Circos software (Fig.4).Among the tion (Supplementary Fig.7a),and 42 Arabidopsis genes orthologous gene pairs of Chinese cabbage and Arabidop- have co-orthologs in Chinese cabbage,these genes were sis,we found more Chinese cabbage MADS-box homolo- preferentially retained after the triplication (Supplemen- gous genes in Arabidopsis chromosome 5 and chromosome tary Fig.7b,c and d).Meanwhile,we found 71 and 60 in I than in other chromosomes.To further obtain insight into paralogous gene pairs in Arabidopsis and Chinese cabbage, SpringerMol Genet Genomics (2015) 290:239–255 245 1 3 the gene number in the Chinese cabbage genome was nota￾bly less than three times the Arabidopsis gene number because some genes were lost during polyploidy speciation. Additionally, both segmental and tandem gene duplications have significant impacts on the expansion and evolution of gene families in plant genomes. In this study, we analysed the ortholog groups between Chinese cabbage and Arabi￾dopsis MADS-box genes using the OrthoMCL program. Then, we identified 67 orthologous gene pairs and 120 co￾orthologous gene pairs in the MADS proteins of these two species (Supplementary Table 6). Their visualisation was performed using the Circos software (Fig. 4). Among the orthologous gene pairs of Chinese cabbage and Arabidop￾sis, we found more Chinese cabbage MADS-box homolo￾gous genes in Arabidopsis chromosome 5 and chromosome 1 than in other chromosomes. To further obtain insight into the correlation of the MADS-box genes in Chinese cabbage and Arabidopsis, the networks of MADS-box genes were constructed using these two species orthologous (Sup￾plementary Fig. 7). Among the orthologous gene pairs of Chinese cabbage and Arabidopsis, 16 Arabidopsis MADS￾box genes were found no ortholog with Chinese cabbage MADS-box genes, these genes have been duplicated in Arabidopsis after the split. Fifty Arabidopsis MADS-box genes have only one ortholog in Chinese cabbage, these genes were present before the split, but two of the three copies have been lost after the B. rapa genome triplica￾tion (Supplementary Fig. 7a), and 42 Arabidopsis genes have co-orthologs in Chinese cabbage, these genes were preferentially retained after the triplication (Supplemen￾tary Fig. 7b, c and d). Meanwhile, we found 71 and 60 in paralogous gene pairs in Arabidopsis and Chinese cabbage, Fig. 2 Phylogenetic tree of Chinese cabbage, Arabidopsis and rice type II MADS-box proteins. Phylogenetic analysis of 182 type II MADS proteins from Chinese cabbage (95), Arabidopsis (46) and rice (41) showing similar groups in all of the plant species. In total, 13 clades with different colours that were formed by type II MADS proteins are also marked (colour figure online)