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

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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(Par̆enicováet 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

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 removedBrMADS genes.

Supplementary Fig. 2. Phylogenetic tree of Chinese cabbage and Arabidopsis MADS proteins. (a): A phylogenetic tree of Arabidopsis MADS proteins. (b): Thephylogeneticrelationships 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).

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.

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