Fig 1.
MADS-box domain of MADSs-box genes in the Brassica napus (BnMADSs) genome.
A multiple alignment analysis was performed using the MAFFT program. The sequence logos are based on the alignments of all type I (Mα, Mβ, and Mγ) and type II (MIKC) B. napus MADS-box domains. Bit scores indicate the information content for each position in the sequence. Black and grey dots indicate 100%- and 90%-conserved residues, respectively.
Fig 2.
Phylogenetic relationships of type II BnMADS proteins investigated in this study.
A neighbor-joining tree representing relationships among 187 BnMADS proteins translated from B. napus and 45 from Arabidopsis are shown. The proteins are clustered into 16 subfamilies. Coloured dots indicate the corresponding intron distribution patterns, as shown in Fig 3.
Fig 3.
Schematic diagram of intron distribution patterns within the K-box of proteins translated from type II BnMADSs.
Alignment of the K-box domains is representative of 7 intron patterns, designated A to G. Intron locations are indicated by white triangles, and the number within each triangle indicates the splicing phases: 0 refers to phase 0; 1 to phase 1; and 2 to phase 2. The number of BnMADSs within each pattern is presented on the left. The correlation between intron distribution patterns and phylogenetic subfamilies is provided in Fig 2.
Fig 4.
Architecture of conserved protein motifs translated from type I BnMADSs.
The percentage of BnMADS proteins with each pattern is presented on the right. Numbers in the colored bar indicate different motifs.
Fig 5.
Chromosomal locations and duplications of BnMADSs.
The chromosome number is indicated above each chromosome. The scale is in megabases (Mb). Genes inherited from B. rapa or B. oleracea genomes are under grey and black backgrounds respectively; genes originating from segmental duplication are underlined by black lines accompanied with the same letter (e.g., a, b, and c); genes arising from homologous exchange (HE) are indicated using black boxes accompanied with the same number (e.g., 1, 2, and 3); and genes originating from tandem duplication are marked with black dots.
Fig 6.
Classification of the cis-elements in BnMADS promoters.
106 Cis-elements were identified in the promoters of all 307 BnMADSs and were classified into three main groups (A–C). The number of type I and type II genes with the same type of cis-element is marked in different colours.
Fig 7.
Expression profiles of type II BnMADSs across different developmental stages and organs.
The genes and their corresponding clade are on the right. The tissues used for expression analysis are indicated at the top of each column. GS, germinate seed; Hy, hypocotyl; Ao, anthocaulus; Ro, root; St, stem; Le, leaf; Cal, calyx; Cap, capillament; Pe, petal; Sta, stamen; Pi, pistil; SP, silique; Se, seed; SC, seed coat; Em, embryo; Co, cotyledon. s, seedling stage; b, bud stage; i, initial flowering stage; and f, full-bloom stage. The time after seed germination is indicated as 24, 48, and 72 h. The number of days after pollination (DAP) is indicated as 3, 19, 21, 30, 40, and 46 d. The colour bar represents log2 expression values (FPKM). The genes with weak or no expression are supplied in S1 Table.