DOI: 10.5061/dryad.b1k526g
title: Total Ortholog Median Matrix (TOMM): an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

description: The increasing number of available genomic data allowed the development of
 phylogenomic analytical tools. Current methods compile information from
 single gene phylogenies, whether based on topologies or multiple sequence
 alignments. Generally, phylogenomic analyses elect gene families or
 genomic regions to construct phylogenomic trees. Here, we presented an
 alternative approach for Phylogenomics, named TOMM (Total Ortholog Median
 Matrix), to construct a representative phylogram composed by amino acid
 distance measures of all pairwise ortholog protein sequence pairs from
 desired species inside a group of organisms. The procedure is divided two
 main steps, (1) ortholog detection and (2) creation of a matrix
 with the median amino acid distance measures of all pairwise orthologous
 sequences. We tested this approach within three different group of
 organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and
 Primates. Our approach was robust and efficacious to reconstruct the
 phylogenetic relationships for the three groups. Moreover, novel branch
 topologies could be achieved, providing insights about some phylogenetic
 relationships between some taxa.
description: <b>Supplemental Figures: S1,
 S2, S3, S4, S5, S6 and
 S7</b> S1-S6: Phylograms using
 different percentiles of the ranked ortholog pairs of 46 species of
 Kinetoplastida protozoa (S1, S2 and S4), different
 cutoff for E-value (S3) and different methods for orthology inference (S5
 and S6). S7: Bar graph showing the
 total number of orthologous identified by the RSD and OrthoMCL algorithms
 for 78 pairs of species combinations used in the analysis, based on 13
 species with sequences retrieved from TriTryp database, as indicated in
 Table 1 ("Proteins sequence source" column). Intersections
 (shared orthologs) and unique orthologs were calculated with gene ID lists
 as input using Venn diagram tool
 (http://bioinformatics.psb.ugent.be/webtools/Venn/). File name: Supplemental_Figures_S1_S2_S3_S4_S5_S6_S7.pdf Supplemental Table 1: Kinetoplastida pairwise matrices Excel spreadsheet containing resulting tables of pairwise orthologs data (pairwise matrices). Sheet "AA distance": aminoacid distance obtained from median value calculated by RSD algorithm. Sheet "Number-50": total number of orthologs identified by RSD algorithm settings of of 0.01 for the blast e-value of acceptance, and the value of 0.8 for the minimum ratio of the smallest sequence to the larger one.   SupplementalTable_S1.xlsx Supplemental Table 2: Hemataphagous Diptera pairwise matrices Excel spreadsheet containing resulting tables of pairwise orthologs data (pairwise matrices). Sheet "AA distance": aminoacid distance obtained from median value calculated by RSD algorithm. Sheet "Number-50": total number of orthologs identified by RSD algorithm settings of of 0.1 for the blast e-value of acceptance, and the value of 0.8 for the minimum ratio of the smallest sequence to the larger one.   SupplementalTable_S2.xlsx Supplemental Table 3: Primates pairwise matrices Excel spreadsheet containing resulting tables of pairwise orthologs data (pairwise matrices). Sheet "AA distance": aminoacid distance obtained from median value calculated by RSD algorithm. Sheet "Number-50": total number of orthologs identified by RSD algorithm settings of of 0.01 for the blast e-value of acceptance, and the value of 0.8 for the minimum ratio of the smallest sequence to the larger one.   SupplementalTable_S3.xlsx <b>Supplemental Table S4: Comparison between orthology detection methods, RSD and OrthoMCL, using 13 species with protein sequences retrieved from TriTryp database.</b>  Intersections (shared orthologs) and unique orthologs were calculated with gene ID lists from each method as input using Venn diagram tool (http://bioinformatics.psb.ugent.be/webtools/Venn/). SupplementalTable_S4.xlsx Supplemental File 1: R scripts Scripts for hclust, pvclust and ape R packages used to build phylograms from amino acid distance matrices.   SupplementalFile1.txt   <b>Supplemental File 2: RSD resulting files (gene IDs) in </b><b>compressed folders</b> The compressed folders named “RSD-Primates”, “RSD-Flies”, RSD-kinetoplastids”, contain text files with gene IDs resulted from RSD searches. Gene IDs for each paired species are tabulated in two columns, where first column indicates IDs from first species and second column indicates IDs from second species. Names of each paired species are abbreviated in the txt file name, using the first three letters for genus plus species, separated by hyphen, e.g.: the AOTNAN-CEBCAP-0.txt file presents gene IDs for <i>Aotus nancymaae </i>in the first column, while in the second column gene IDs belong to <i>Cebus capucinus</i>. The abbreviation for all organisms is supplied in Excel files Supplemental Tables S1, S2 and S3, under sheet “Abbreviation”. File name: Supplemental_File2.tar.gz