Journal: The Biochemical journal

Article Title: Molecular biology, genetics and biochemistry of the repulsive guidance molecule family

doi: 10.1042/BJ20090978

Figure Lengend Snippet: Evolutionary trees have been derived from the protein translation of well-annotated RGM DNA sequences in which the mRNA and gene agrees. Methods of analysis are as follows: seven separate MSAs (multiple sequence alignments) of full-length RGM proteins were performed with MUSCLE [14], Clustal-W [75] or hand alignment, followed by direct submission or a codon-optimized alignment through PAL2NAL [76]. Either protein MSAs or codon-based alignments were submitted to several phylogenetic methods, including neighbour joining with unrooted and rooted trees (via MacVector), maximum likelihood [77,78] (with and without Bootstrap methods on neighbour joining and maximum likelihood) and Bayesian [79,80] analysis. (A) RGM family phylogeny using an unrooted maximum likelihood method, displaying a distance of 0.1 amino acid substitutions per position (scale bar). (B) RGM family cladogram derived from the neighbour joining method (Poisson-correction with gaps distributed proportionally) rooted with zebrafish (Dre) RGMc, displaying bootstrap values as percentage of 5000 replications supporting that branch on the cladogram. Species abbreviations for (A) and (B) may be found in Table 1. For both (A) and (B), the putative ancestral RGM is highlighted in green and the ancestral gene to RGMa and RGMb is shown in blue. Phylogeny and cladogram created using Pal2NAL [76], Selection Server [81], Phylogeny.fr [78], PhyML 3.0 [77], TreeDyn [82] and MacVector v7.2.3.

Article Snippet: Phylogeny and cladogram created using Pal2NAL [ 76 ], Selection Server [ 81 ], Phylogeny.fr [ 78 ], PhyML 3.0 [ 77 ], TreeDyn [ 82 ] and MacVector v7.2.3.

Techniques: Derivative Assay, Sequencing, Selection