Figure 1.
The protein sequence alignment of the MRF family.
A) The domain differences of the MRFs gene family. B) The sequence alignment of the HLH domains of representative MRFs from nematodes to humans. C) The sequence alignment of the C-terminal sequences of representative vertebrate MRFs. The amino acid sequence SXXTSPXSNCSDGM and SSLDCLSXIVXRIT are conserved in the MYF5 domains of MyoD and Myf5.
Figure 2.
Estimation of positive selection during MRFs evolution.
The branches were estimated for positive selection in the following: A) vertebrate MRFs phylogeny, B) vertebrate MyoD; and, C) vertebrate MyoG. All the branches with a ω-ratio significantly greater than 1 are marked with arrows and letters corresponding to those in Table 1 and Table 2.
Figure 3.
Mapping positive selection sites for the functional divergence between myogenic determination factors and myogenic differentiation factors.
A, B) Maps of the positive selection sites identified using all vertebrate MRF sequences. The stars represent the 11 sites under positive selection identified by M8 versus M7 in Table 1. C, D) The map sites under positive selection responsible for the functional divergence between myogenic determination factors and myogenic differentiation factors. The sites with Bayes Empirical Bayes (BEB) probabilities>0.95 represent the sites under positive selection in Table 1. The yellow balls represent the sites located in the BASIC domain, and black balls represent the sites located in the MYF5 domain and C-terminus. The position of positive selection sites on the protein three-dimensional MRFs model are marked according to the sequences of human MyoD. E) Twenty-nine residues with a posterior ratio more than 8 have been observed as Type I functional divergence.
Table 1.
Likelihood Ratio Tests for the Positive Selection on all the MRF genes.
Figure 4.
Mapping positive selection sites for the functional divergence among members of MRFs.
A) Positive selection sites identified from lineages of vertebrate MRFs. B) Positive selection sites identified from lineages of vertebrate MyoD or MyoG. C) Positive selection sites identified from the mammalian MyoG sequences. The sites with Bayes Empirical Bayes (BEB) probabilities >0.95 represent the sites under positive selection in Table 2.
Table 2.
Likelihood Ratio Tests for the Positive Selection on each of the four MRFs.
Figure 5.
Nonsynonymous substitution rate (dN) and synonymous substitution rate (dS) of the three domains in the MRFs.
A), B) and C) represent the dN/dS differences of the three domains of the MRFs in vertebrates, mammals and Myf5 genes, respectively. D), E) and F) represent the dN/dS differences of the four MRFs genes in their HLH, BASIC and MYF5 domains, respectively.