title: Ortholog-Finder: A Tool for Constructing an Ortholog Data Set.
abstract: Orthologs are widely used for phylogenetic analysis of species; however, identifying genuine orthologs among distantly related species is challenging, because genes obtained through horizontal gene transfer (HGT) and out-paralogs derived from gene duplication before speciation are often present among the predicted orthologs. We developed a program, "Ortholog-Finder," to obtain ortholog data sets for performing phylogenetic analysis by using all open-reading frame data of species. The program includes five processes for minimizing the effects of HGT and out-paralogs in phylogeny construction: 1) HGT filtering: Genes derived from HGT could be detected and deleted from the initial sequence data set by examining their base compositions. 2) Out-paralog filtering: Out-paralogs are detected and deleted from the data set based on sequence similarity. 3) Classification of phylogenetic trees: Phylogenetic trees generated for ortholog candidates are classified as monophyletic or polyphyletic trees. 4) Tree splitting: Polyphyletic trees are bisected to obtain monophyletic trees and remove HGT genes and out-paralogs. 5) Threshold changing: Out-paralogs are further excluded from the data set based on the difference in the similarity scores of genuine orthologs and out-paralogs. We examined how out-paralogs and HGTs affected phylogenetic trees constructed for species based on ortholog data sets obtained by Ortholog-Finder with the use of simulation data, and we determined the effects of confounding factors. We then used Ortholog-Finder in phylogeny construction for 12 Gram-positive bacteria from two phyla and validated each node of the constructed tree by comparison with individually constructed ortholog trees.
authors.affiliation: Department of Biological and Environmental Science, Shizuoka University, Japan horiike.tokumasa@shizuoka.ac.jp.
authors.forename: Tokumasa
authors.initials: T
authors.lastname: Horiike
authors.affiliation: The Genome Institute, Japanese Foundation of Cancer Research, Tokyo, Japan.
authors.forename: Ryoichi
authors.initials: R
authors.lastname: Minai
authors.affiliation: Department of Economics, Chiba University of Commerce, Ichikawa, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyata
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, Kanagawa, Japan.
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: School of New Sciences, Daegu Gyoungbook Institute of Science and Technology, Daegu, Republic of Korea.
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Tateno
mesh_terms: D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D006094:Gram-Positive Bacteria / Q000145:classification / Q000235:genetics; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: eukaryote; horizontal gene transfer; ortholog; out-paralog; phylogenetic analysis; prokaryote