Fig. 3

Structure, distribution, and regulatory elements of SsR2R3-MYB genes. a Comparison of gene structure between S. spontaneum and S. bicolor based on the phylogenetic tree. ClustalX performed the sequence alignment of SsR2R3-MYB and SbR2R3-MYB proteins, and the Phylogenetic tree was constructed using MEGA 7.0 with Neighbor-Joining (NJ) method, 1000 bootstrap replicates, Pairwise deletion, and Bootstrap values on the nodes. SsMYB gene names are marked black, and SbMYB gene names are marked red. Gene sequences were modified to start at the transcription initiation site (ATG), and gene structures were displayed using GSDS2.0 (http://gsds.cbi.pku.edu.cn/). The CDS sequence and intron were represented as fine lines and yellow cylinders, and green cylinders highlighted the MYB domain. The first subgroup was presented here when the estimated phylogenetic relationship of S. spontaneum and S. bicolor and others were shown in Figure S2. b Cis-regulatory elements of SsR2R3-MYB gene promoters with diversified plant biological functions. The functions of the predicted cis-regulatory elements covered four main categories: stress response, hormone response, light response, plant growth, and metabolism. The x-axis showed divers plant biological functions, and the y-axis indicated the number of a specific category of genes in that main category. The red rectangle represented the genes containing more than six elements involved in regulating a particular plant function. c Distribution of SsR2R3-MYB gene members in S. spontaneum genome. 202 SsR2R3-MYB genes were named according to their physical position on the chromosome and tagged in red font. Yellow font indicated chromosome name, and chromosome was represented as hollow cylinders with length scale (bp) on the left. The green spots displayed a gene enrichment cluster