Computational protocol: The Evolution and Appearance of C3 Duplications in Fish Originate an Exclusive Teleost c3 Gene Form with Anti-Inflammatory Activity

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Protocol publication

[…] An exhaustive BLAST search was performed against the Danio rerio full genome (version Zv9) with the available human C3 and zebrafish c3 sequences that were retrieved from the public NCBI nucleotide database (http://www.ncbi.nlm.nih.gov/nucleotide). Similarities and identities between the corresponding protein sequences were calculated with MatGAT 2.02 . Structural characterizations were investigated with the NCBI online Conserved Domain Database (CDD) .Additional fish C3 and C5 protein sequences were retrieved from published genomes with the Ensembl Genome Browser, version 69 (). The sequence alignment was performed with the MAFFT online server according to the E-INS-i strategy . Ambiguously aligned columns were pruned with Gblocks 0.91b . The best-fit model of amino acid replacement was selected according to the Akaike Information Criterion (AIC) with ProtTest 3.2 . The c3–c5 gene family tree was estimated with jPrime 0.2.0 , in which 4 independent MCMC runs, each consisting of 1,000,000 iterations, were sampled once every 200 iterations. After discarding the first 500 samples for each run as burn-in, the final gene tree was obtained as a weighted consensus majority-rule tree from the 4 runs with MrBayes 3.2.1 , .To identify gene duplications and loss events during the evolution of the c3–c5 gene family, a reconciliation , of the c3–c5 tree with fish phylogeny was performed. Although the evolutionary relationships among fish species are not well resolved , in this study, a species tree coherent with the accepted taxonomic relationships among teleost species was selected (). The divergence times among fish species were retrieved from the TimeTree database . The most parsimonious reconciliation of the estimated gene tree and the species tree was performed with Notung 2.6 , and represented with FigTree v1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/) and PrimeTV . Synteny was investigated with Genomicus v69.01 . […]

Pipeline specifications

Software tools MatGAT, MAFFT, Gblocks, ProtTest, MrBayes, Notung, FigTree, primetv
Databases CDD Genomicus
Application Phylogenetics
Organisms Danio rerio