FIGURE 2.

Comparative phylogenetic analysis-based subfamily classifications of wheat MADS-box genes. Arabidopsis, rice, and wheat MADS-box proteins were MAFFT aligned (Katoh and Standley, 2013; Katoh et al., 2018), maximum likelihood phylogenies inferred using I_Q-T_REE software (Nguyen et al., 2015) and final trees visualized with MEGA7 (Kumar et al., 2016). Separate phylogenetic trees were inferred among Arabidopsis, rice, and wheat MIKC-type (A) and M-type (B) proteins. Wheat MADS-box genes are highlighted with solid black circles. Only bootstrap values ≥ 50%, as calculated from 1,000 replicates, could be displayed on the tree nodes. Subfamily-specific colouring was adopted for differentiating the different subfamilies. Subfamily names (outer bands) were given by following the subfamily classifications in Arabidopsis and/or major grass species (Gramzow and Theißen, 2015). Alternate gene names used in previous studies are also provided in Supplementary Table S4.