Figure 3
Phylogenetic tree of jawed vertebrate Bmp16 genes and alignment of their deduced amino acid sequences. (A) Tree inference is based on the Dayhoff + Γ4 (shape parameter of gamma distribution α = 0.50) and an alignment of 96 amino acids. Support values at nodes are shown in order, bootstrap probabilities in the ML analysis and in the NJ analysis, and posterior probabilities in the Bayesian tree inference. Only bootstrap values no less than 70 in the ML analysis are shown. See Table S1 for accession IDs of included sequences. (B) Presences and presumed absences of Bmp16 genes in major vertebrate lineages. Inferred secondary gene losses are indicated in the species tree with red crosses. Question marks indicate uncertainty about absence of Bmp16 genes due to limited sequence resources. The phylogenetic position of turtles is based on existing literature44,47,48,49,77. (C) Conservation of the two proteolytic cleavage sites S1 and S2. The minimal motif Arg-X-X-Arg (R-X-X-R) is conserved in all BMP2/4/16 proteins, except for a few BMP16 proteins. The conservation level of the cleavage sites was visualized using the software WebLogo (URL: http://weblogo.berkeley.edu71). (D) Alignment of the C-terminus of diverse BMP16 and human BMP2 and -4 proteins. Cysteine residues (‘C’) that are involved in the formation of the cysteine-knot motif are shown in bold. This amino acid site is conserved throughout the alignment, except for A. carolinensis BMP16 whose fourth cysteine is substituted by a serine residue (‘S’).
