Computational protocol: Molecular Evolution of MDM1, a “Duplication-Resistant” Gene in Vertebrates

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Protocol publication

[…] Sequences of human and zebrafish were identified through searches of the NCBI database using the gene symbol for MDM1. The remaining MDM1 protein sequences were identified through BLASTp in Ensembl and NCBI using the human and zebrafish MDM1 sequences as queries with default settings [, ]. Blink (BLAST Link) in NCBI was employed to identify/verify the MDM1 in closely related taxa from the pre-computed sequence alignments. Representative MDM1 sequences from the major metazoan taxa were selected based on their taxonomic positions. Whenever there were multiple isoforms, the longest sequence was chosen for analysis. The final MDM1 protein accession numbers and species are listed in the .The multiple sequence alignments were generated with the MUSCLE program [], and can be found in the . Phylogenetic analyses using the multiple protein alignments were conducted with Baysian analysis (BP), Maximum Likelihood (ML) and Neighbor Joining (NJ) methods [–]. Best fitting evolutionary models were tested in the MEGA 6.06 program using maximum likelihood and default parameters []. The models with the lowest BIC scores (Bayesian Information Criterion) are considered to describe the substitution pattern the best, and in our studies we chose JTT+G (α = 2.087). For BP phylogenetic analysis, 10 million generations were run using the following parameters with MrBayes 3.2.6: nruns = 2, nchains = 4, aamodel = fixed (Jones), rates = gamma ngammacat = 8, samplefreq = 500, burninfrac = 0.25. For ML phylogenetic analysis, PHYML 3.1 [] was chosen using the following parameters: datatype = AA; model = JTT, gamma = yes, gamma distribution parameter = estimate (α = 1.997); bootstrap = 1000. NJ analysis was carried out using MEGA 6.06 with the following parameters: Test of phylogeny = bootstrap method, No. of Bootstrap Replications = 10,000, Substitution Type = Amino Acid, Model = JTT, Rates among sites = Gamma Distribution (G), Gamma Parameter = 2.087, Gaps/Missing Data Treatment = Pairwise and/or complete deletion. BP and ML phylogenetic trees were visualized and displayed with FigTree V1.4.2 (http://tree.bio.ed.ac.uk/software/figtree).Selected vertebrate MDM1 genomic structure and synteny analysis were performed using the UCSC genome browser and Ensembl database: elephant shark (Callorhinchus milii) calMil1; zebrafish (Danio rerio) GRCz10; chicken (Gallus gallus) Galgal4; human (Homo sapiens) GRCh38.p3; spotted gar (Lepisosteus oculatus) LepOcu1; mouse (Mus musculus) GRCm38.p4; Western clawed frog (Xenopus tropicalis) JGI 4.2; platyfih (Xiphophorus maculatus) Xipmac4.4.2; Japanese medaka (Oryzias latipes) HdrR. […]

Pipeline specifications

Software tools BLASTP, MUSCLE, MEGA, MrBayes, PhyML, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Danio rerio, Mus musculus
Diseases Neoplasms, Retinal Degeneration