Computational protocol: The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes

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Protocol publication

[…] Sequences for members of the TGFβ superfamily were retrieved from the Ensembl genome database (version 53; []) and NCBI Protein database, by running Blastp [] using mammalian Bmp2 peptide sequences as queries. In parallel, peptide sequences of Branchiostoma floridae were also downloaded from Joint Genome institute (JGI; http://genome.jgi-psf.org/Brafl1/Brafl1.download.ftp.html), and used as a target of a Blastp search. An optimal multiple alignment of the retrieved amino acid sequences and those sequenced in this study was constructed using the alignment editor XCED, in which the MAFFT program is implemented []. [...] Molecular phylogenetic trees were inferred using the regions that were unambiguously aligned with no gaps. The neighbor-joining tree reconstruction [] was processed using XCED. To calculate the support values for the molecular phylogenetic tree shown in Figures and , we used PhyML [] and MrBayes 3.1 []. Bootstrap probabilities were obtained with 100 resamplings. To investigate the phylogenetic relationship between Bmp2/4/16 and P. marinus genes (Table ), the maximum-likelihood (ML) tree was inferred using Tree-Puzzle [], assuming JTT+I+Γ4 model (shape parameter of the gamma distribution α = 0.47). In this ML analysis, we performed an exhaustive search of the ML tree in the 'user defined trees' mode of Tree-Puzzle with all 945 possible topologies consisting of seven OTUs, namely, gnathostome Bmp2, gnathostome Bmp4, teleost bmp16, P. marinus PmBmp2/4-A, P. marinus PmBmp2/4-B, P. marinus PmBmp2/4-C and outgroup. Phylogenetic relationships within individual OTUs were constrained according to generally accepted phylogenetic relationships of relevant species. Statistical tests for evaluation of alternative tree topologies were performed using CONSEL []. […]

Pipeline specifications

Software tools BLASTP, OMA, MAFFT, PhyML, MrBayes, TREE-PUZZLE, CONSEL
Databases NCBI Protein
Applications Phylogenetics, Amino acid sequence alignment
Organisms Danio rerio, Caenorhabditis elegans