Computational protocol: Placenta-Specific Protein 1 Is Conserved throughout the Placentalia under Purifying Selection

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Protocol publication

[…] Using the PLAC1 cDNA sequence from human PLAC1 mRNA (NM_021796) as the starting point, 42 mammalian genomes in ENSEMBL were screened via BLAST. For this round, default parameters were employed and only local sequence dissimilarities were accepted. Among these, the PLAC1 coding region could be unambiguously identified in a total of 25 species representing nine crown orders of the Placentalia. Crown orders are Primates, represented by nine species (human, Homo sapiens (Has); chimpanzee, Pan troglodytes (Ptr); gorilla, Gorilla gorilla (Ggo); orangutan, Pongo abelii (Pab); gibbon, Nomascus leucogenys (Nle); rhesus macaque, Macaca mulatta (Mml); baboon, Papio hamadryas (Pha); marmoset, Callithrix jacchus (Cja); and galago, Otolemur garnettii (Oga)); Rodentia, represented by four species (mouse, Mus musculus (Mmu); rat, Rattus norvegicus (Rno); squirrel, Ictidomys tridecemlineatus (Itr); and kangaroo rat, Dipodomys ordii (Dor)); Carnivora, represented by four species (dog, Canis familiaris (Cfa); cat, Felis catus (Fca); panda, Ailuropoda melanoleuca (Ame); and ferret, Mustela putorius (Mpu)); Artiodactyla, represented by three species (cow, Bos Taurus (Bta); pig, Sus scrofa (Ssc); and Dolphin, Tursiops truncatus (Ttr)); Perissodactyla, represented by horse, Equus caballus (Eca); Afrotheria, represented by elephant, Loxodonta africana (Laf); Chiroptera, represented by the microbat, Myotis lucifugus (Mlu); Lagomorpha, represented by rabbit, Oryctolagus cuniculus (Ocu); and Scandentia, represented by the tree shrew, Tupaia belangeri (Tbe).The 25 PLAC1 coding region DNA sequences were aligned using MUSCLE (v3.7) []. The alignment was curated with Gblocks (v0.91b) [] and a phylogenetic tree constructed using the maximum likelihood method in PhyML (v3.0 aLRT) [, ]. Support for the tree was determined by bootstrap and the tree rendered in TreeDyn (v1983) []. All of the above analyses were implemented in Phylogeny.fr using default parameters [].Amino acid translations from the 25 coding region DNA sequences were carried out and used in tandem with the DNA sequences to estimate selection. Selection on both intact PLAC1 protein and PLAC1 functional domains, represented as dN/dS, was determined for species pairs using PAL2NAL [] in which the dN/dS ratio is computed from the synonymous (dS) and nonsynonymous (dN) substitution rates calculated by codeml in PAML []. […]

Pipeline specifications

Software tools MUSCLE, Gblocks, PhyML, TreeDyn, Phylogeny.fr, PAL2NAL, PAML
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Homo sapiens