Computational protocol: The evolutionary conservation of the A Disintegrin-like and Metalloproteinase domain with Thrombospondin-1 motif metzincins across vertebrate species and their expression in teleost zebrafish

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Protocol publication

[…] Protein sequences of ADAMTS family members across Chordata were retrieved from 3 databases (DB): Ensembl (v70), Uniprot (SwissProt + TrEMBL) and nr-prot (NCBI). Sequences from representative species were aligned using MAFFT []. Using ad hoc scripts and manual selection, multiple sequences in each species were trimmed, retaining the best-annotated sequences in those alignments. To root the phylogenies, when available and pending their ability to be aligned, the sequences from Ciona intestinalis, Ciona savignyi, Branchiostoma floridae, and from outside Phylum Chordata (e.g. Strongylocentrotus purpuratus, Saccoglossus kowaleskii, Crassostrea gigas or insects) were used. Phylogenetic analyses were achieved using the methods of Neighbor-Joining (BioNJ) [] implemented in SeaView [], or run under a WAG model with estimated gamma distribution parameter for the Maximum Likelihood (PhyML) [], both of them with 1000 bootstrap iterations. In addition to our phylogenetic analyses, the orthologous relationship to each of these genes in the vertebrates was verified using Genomicus [,], which allows the visualization of orthology by synteny from the genomic information provided by the Ensembl database. BioNJ values (available upon request) corroborated those obtained by PhyML but were not added to keep clarity in the figures.We also looked for adamts proteins beyond Chordata and to discriminate them from other metalloproteinases such as those encoding ADAM genes, common protein sequences of each ADAMTS encompassing the metalloproteinase, the disintegrin-like, the first TSP type-1 and the cysteine-rich domains were selected. Each of these sequences was used in BLASTP (blosum45 matrix used) searching of the nr protein database at NCBI restricted to the non-vertebrate Opisthokonta species. Retrieved protein sequences were pooled together with the vertebrate ADAMTS sequences, with sequences retained that aligned best all along these vertebrate sequences. This very stringent selection process was important to understand the relationship of all ADAMTS in species very distantly related and with different modes of development, and obtain an overview of the whole evolutionary history; the caveat being that it may have discarded ADAMTS genes that followed a different evolutionary path in other species, such as the ecdysozoans and the lophotrochozoans. […]

Pipeline specifications

Software tools MAFFT, SeaView, PhyML, BLASTP
Application Phylogenetics
Organisms Danio rerio, Homo sapiens
Chemicals Zinc