Genome-wide analysis of the MADS-box gene family in Chinese cabbage (Brassica
rapa ssp. pekinensis)
Weike Duan • Xiaoming Song • Tongkun Liu • Zhinan Huang • Jun Ren • Xilin Hou•
Ying Li*
1. State Key Laboratory of Crop Genetics and Germplasm Enhancement. 2. Key laboratory
of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of
Agriculture, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
＊To whom correspondence should be addressed: yingli@njau.edu.cn
Tel.: +86 025 8439 5756
Fax: +86 025 8439 5262
Supplementary data legends
Supplementary Table 1: The result about Chinese cabbage MADS genes by Hmm Search
and the information of them
Supplementary Table 2: Information of MADS genes in Oryza sativa (Arora et al. 2007),
Zea mays, Sorghum bicolor (Zhao et al. 2011), Vitis vinifra (Díaz-Riquelme et al. 2009),
Citrus clementina, Citrus sinensis (Hou et al. 2013), Arabidopsis thaliana (Par̆ enicová et al.
2003), Cucumls sativus (Hu et al. 2012), Glycine max, Medicago truncatula (Fan et al. 2013),
Populus trichocarpa (Leseberg et al. 2006), Physcomitrella patens (Barker et al. 2013),
Selaginella moellendorffii (Gramzow et al. 2012) in the previous reports
1
Supplementary Table 3: Information of MADS genes in Volvox carteri, Physcomitrella
paters, Aquilegia coerulea, Solanum lycopersicum, Solanum tuberosum, Thellungiella
halophila, Capsella rubella, Arabidopsis lyrata, Prunus persica in this work
Supplementary Table 4: Identification of homoeologous MADS-box genes between A.
thaliana and three subgenomes in B. rapa
Supplementary Table 5: The orthologous gene pairs and co-orthologous gene pairs in
MADS-box proteins of Chinese cabbage and Arabidopsis, the paralogous gene pairs in
these two species
Supplementary Table 6: The subgroups of BrMADS genes and their best match with
Arabidopsis
Supplementary Table 7: The Blast resut of BrMADS genes
Supplementary Table 8: Ks Values for Pairs of MADS-box Genes in Chinese cabbage
Supplementary Table 9: Estimates of Evolutionary Divergence between Sequences
Supplementary Table 10: The FPKM values of B. rapa MADS-box genes
Supplementary Table 11: List of primers used for qRT-PCR analysis and their sequence,
amplicon size, primer length, primer designing site and amplicon sequence
Supplementary Table 12: Relative expression of BrMADS genes in different treatments by
qRT-PCR
Supplementary Table 13: Relative expression of duplication BrMIKC genes in different
treatments by qRT-PCR
Supplementary Fig. 1. The protein structure and multiple sequence alignment result of the
removed BrMADS genes.
Supplementary Fig. 2. Phylogenetic tree of Chinese cabbage and Arabidopsis MADS
proteins. (a): A phylogenetic tree of Arabidopsis MADS proteins. (b): The phylogenetic
2
relationships of Chinese cabbage and Arabidopsis MADS proteins. (c): Phylogenetic tree of
Chinese cabbage, Arabidopsis, rice soybean and grapevine MADS proteins.The tree is
divided into five phylogenetic subgroups, which are designated as MIKCC, MIKC*, Mα, Mβ
and Mγ.
Supplementary Fig. 3. Retention of type I and type II BrMADS genes and percentages of
each BrMADS subgroup genes. (a): Retention by number of homoeologous copies in the
syntenic region between Arabidopsis and B. rapa. (b): Retention of homoeologs among the
three subgenomes of B. rapa. (c): The number and percentages of each BrMADS subgroup
genes.
Supplementary Fig. 4. Phylogenetic tree of Chinese cabbage, Arabidopsis and rice type I
MADS-box proteins. The tree is divided into three phylogenetic subgroups, which are
designated as Mα, Mβ and Mγ.
Supplementary Fig. 5. Phylogenetic relationships and conserved motif compositions of
Chinese cabbage and Arabidopsis type I MADS proteins. The neighbour-joining tree of
Chinese cabbage and Arabidopsis type I MADS-box genes and their motif locations.
Supplementary Fig. 6. Phylogenetic relationships, conserved motif compositions, gene
structure and tissue-specific expression of BrMADS genes. Phylogenetic tree: A
neighbour-joining tree of Chinese cabbage MADS-box genes. Multiple sequence alignment
of full-length MADS proteins was performed using the ClustalW2 program, and the
phylogenetic tree was constructed using the MEGA5.2 software by the neighbour-joining
method with 1000 bootstrap replicates. Gene structure: Distribution of the exons and introns
of BrMADS genes using the CDS and DNA sequences according to research using the tool
GSDS. Protein structure: Distribution of conserved motifs in Chinese cabbage MADS
protein identified using the MEME search tool. Different motifs are indicated by different
colours, and the names of all members and combined p-values are on the left. Expression
pattern: The expression of BrMADS genes in six tissues (root, stem, leaf, flower, silique and
callus).
3
Supplementary Fig. 7. The networks of MADS-box genes in Chinese cabbage and
Arabidopsis. This interrelation network has been constructed using Chinese cabbage and
Arabidopsis orthologous gene pairs. (a): One orthologous gene pair between Chinese
cabbage and Arabidopsis. (b): Two orthologous gene pairs between Chinese cabbage and
Arabidopsis. (c): Three or more than three orthologous gene pairs between Chinese
cabbage and Arabidopsis. (d): Statistics of the number of orthologous gene pairs between
Chinese cabbage and Arabidopsis.
Supplementary Fig. 8. The phylogenetic relationship, gene structure and protein structure
of the BrMADS duplicated genes.
References
Arora R, Agarwal P, Ray S, Singh A, Singh V, Tyagi A, Kapoor S (2007). MADS-box gene
family in rice: genome-wide identification, organization and expression profiling during
reproductive development and stress. BMC Genomics 8:242
Barker E, Ashton N (2013). A parsimonious model of lineage-specific expansion of
MADS-box genes in Physcomitrella patens. Plant Cell Rep 32: 1161-1177
Díaz-Riquelme J, Lijavetzky D, Martínez-Zapater JM, Carmona MJ (2009). Genome-wide
analysis of MIKCC-type MADS box genes in grapevine. Plant Physiol 149:354-369.
Fan CM, Wang X, Wang YW, Hu RB, Zhang XM, Chen JX, Fu YF (2013). Genome-wide
expression analysis of soybean MADS genes showing potential function in the seed
development. PloS One 8:e62288
Gramzow L, Barker E, Schulz C, Ambrose B, Ashton N, Theißen G, Litt A (2012).
Selaginella genome analysis-entering the “homoplasy heaven” of the MADS world.
Front Plant Sci 3: 214
Hou XJ, Liu SR, Khan MRG, Hu CG, Zhang JZ (2013). Genome-wide identification,
classification, expression profiling, and SSR marker development of the MADS-Box
gene family in citrus. Plant Mol Biol Rep 32(1): 28-41
4
Hu L, Liu S, Somers D (2012). Genome-wide analysis of the MADS-box gene family in
cucumber. Genome 55:245-256
Leseberg CH, Li A, Kang H, Duvall M, Mao L (2006). Genome-wide analysis of the
MADS-box gene family in Populus trichocarpa. Gene 378:84-94
Par̆ enicová L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram
RM, Kater MM, Davies B (2003). Molecular and phylogenetic analyses of the complete
MADS-box transcription factor family in Arabidopsis new openings to the MADS world.
Plant Cell 15:1538-1551
Zhao Y, Li X, Chen W, Peng X, Cheng X, Zhu S, Cheng B (2011). Whole-genome survey
and characterization of MADS-box gene family in maize and sorghum. Plant Cell Tiss
Org 105:159-173
5