DOI: 10.6084/m9.figshare.23230562.v1
title: Supplementary Material, Dataset S2: phylogenies and alignments

description: Supplementary Dataset S2This is a folder containing the alignments (original and filtered) and the phylogenetic trees used in:<pre><pre>Research manuscript: "Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution"<br><br>Accepted for publication in <i>Molecular Biology and Evolution</i>, Sep 2023.<br><br>Authors: Katayoun Kazemzadeh, Ludovic Pelosi, Clothilde Chenal, Sophie-Carole Chobert, Mahmoud Hajj Chehade, Margaux Jullien, Laura Flandrin, William Schmitt, Qiqi He, Emma Bouvet, Manon Jarzynka, Nelle Varoquaux, Ivan Junier, Fabien Pierrel*, Sophie S Abby*<br>* corresponding authors<br> <br>Address: Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France<br> <br></pre></pre>DescriptionThe folder architecture is as follows:<pre><pre>.<br>├── Coq7<br>│ ├── big<br>│ ├── exp<br>│ └── other<br>├── UQ-FMO<br>│ ├── aln_fig_sup<br>│ ├── big<br>│ │ ├── UbiFHI<br>│ │ ├── UbiLN<br>│ │ └── UbiM<br>│ ├── exp<br>│ └── root<br>│ ├── all-sequences<br>│ ├── all-sequences-no-UbiN<br>│ └── all-sequences-no-UbiN-no-LgBranchUbiL<br>└── iTol_annotations<br></pre></pre>Within each sub-folder are presented the filtered and unfiltered alignments, as well as the phylogenetic trees obtained from the filtered alignments.The material is organized by protein families: UQ-FMO or Coq7. Then, for each of them is presented the tree obtained from:a large dataset of representative sequences: <code>big</code> folders (all annotated sequences for UbiM)the subset of experimentally validated sequences: <code>exp</code> foldersIn addition we introduced:a rooted tree analysis for UQ-FMO in the <code>UQ-FMO/root</code> sub-folder, based on the analysis of experimentally tested UQ-FMO with a set of outgroup FMO sequences - these are described in Text S1 and appear on Figure S2.folder <code>all-sequences</code> contains a set of representative UQ-FMO + FMO class A outgroupfolder <code>all-sequences-no-UbiN</code> contains a set of representative UQ-FMO + FMO class A outgroup, UbiN sequences excludedfolder <code>all-sequences-no-UbiN-no-LgBranchUbiL</code> contains a set of representative UQ-FMO + FMO class A outgroup, UbiN sequences excluded, UbiL sequence from Rickettsiales, Holosporales and Pelagibacterales excluded.a phylogenetic analysis for Coq7 and homologs in the <code>Coq7/other</code> sub-folder - these are described in Text S2 and appear on Figure S3A.the alignment underlying Figure S6 presenting the conserved features of experimentally tested sequences in the <code>UQ-FMO/aln_fig_sup</code> folder.Finally, annotation files for the enzymes and taxonomy are provided in the <code>iTol_annotations</code> folder. Within the <code>iTol_annotations</code> folder, there are:1_annot_genes_itol.txt =&gt; UQ-hydroxylase annotation2_annot_taxo-class_itol_Aug-2023.txt =&gt; Taxonomic annotation at the class level3_annot_taxo-order_itol_Aug-2023.txt =&gt; Taxonomic annotation at the order level4_annot_highlight_exp_seqs.txt =&gt; Sequences experimentally validated5_annot_leaflabels-keep-labels_itol.txt =&gt; Labels for all sequences (species name and sequence ID)