Supplementary Material, Dataset S2: phylogenies and alignments

Supplementary Dataset S2This is a folder containing the alignments (original and filtered) and the phylogenetic trees used in:Research manuscript: "Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution"Accepted for publication in Molecular Biology and Evolution, Sep 2023.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** corresponding authors Address: Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France DescriptionThe folder architecture is as follows:.├── Coq7│ ├── big│ ├── exp│ └── other├── UQ-FMO│ ├── aln_fig_sup│ ├── big│ │ ├── UbiFHI│ │ ├── UbiLN│ │ └── UbiM│ ├── exp│ └── root│ ├── all-sequences│ ├── all-sequences-no-UbiN│ └── all-sequences-no-UbiN-no-LgBranchUbiL└── iTol_annotationsWithin 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: big folders (all annotated sequences for UbiM)the subset of experimentally validated sequences: exp foldersIn addition we introduced:a rooted tree analysis for UQ-FMO in the UQ-FMO/root 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 all-sequences contains a set of representative UQ-FMO + FMO class A outgroupfolder all-sequences-no-UbiN contains a set of representative UQ-FMO + FMO class A outgroup, UbiN sequences excludedfolder all-sequences-no-UbiN-no-LgBranchUbiL 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 Coq7/other 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 UQ-FMO/aln_fig_sup folder.Finally, annotation files for the enzymes and taxonomy are provided in the iTol_annotations folder. Within the iTol_annotations folder, there are:1_annot_genes_itol.txt => UQ-hydroxylase annotation2_annot_taxo-class_itol_Aug-2023.txt => Taxonomic annotation at the class level3_annot_taxo-order_itol_Aug-2023.txt => Taxonomic annotation at the order level4_annot_highlight_exp_seqs.txt => Sequences experimentally validated5_annot_leaflabels-keep-labels_itol.txt => Labels for all sequences (species name and sequence ID)