Supplementary Data for Farrell, Nesbø and Zhaxybayeva (2023)

<strong>16SrRNA TreesandPuzzle.zip:</strong> <strong>16SrRNA_describedSpecies_trimmed.aln: </strong><em>16S rRNA gene alignment for described Thermotogota species, trimmed; used in likelihood mapping analyses presented in the Supplementary Figures 2A and 2B</em> <strong>16SrRNA_describedSpecies_iqtreeX2Heterogeneity.txt: </strong><em>Text file of X^2 test of heterogeneity for the described Thermotogota species alignment</em> <strong>16Sr16SrRNA_withClones.aln: </strong><em>16S rRNA gene alignment with environmental sequences included; used for trees in Supplementary Figures 1A and 1B.</em> <strong>16SrRNA_withclones.tree: </strong><em>Tree in Newick format for Supplementary Figure 1A</em> <strong>16SrRNA_withclones_iqtreeX2Heterogeneity.txt: </strong><em>Text file of X^2 test of heterogeneity for tree with environmental sequences as shown in Supplementary Figure 1A</em> <strong>16SrRNA_clones_nhPhymlEq.tree: </strong><em>Tree in Newick format for Supplementary Figure 1B</em> <br> <strong>Ribosomal_Proteins_Analyses.zip:</strong> <strong>concat_rprotTree_DescribedSpeciesStrains.aln: </strong><em>Concatenated alignment of 50 ribosomal proteins from described Thermotogota species; used for tree in Supplementary Figure 3</em> <strong>concat_rprotTree_DescribedSpeciesStrains.tree: </strong><em>Tree in Newick format for Supplementary Figure 3</em> <strong>concat_rprot_withMAGs.aln: </strong><em>Concatenated alignment of 50 ribosomal proteins from Thermotogota described species and MAGs; used for tree in Supplementary Figure 4</em> <strong>concat_rprot_withMAGs.tree: </strong><em>Tree in Newick format for Supplementary Figure 4</em> <strong>individual_Rprot_alignments.zip: </strong><em>Alignment and Tree-Puzzle output file for each of the 50 ribosomal proteins </em> <br> <strong>Single_Copy_Core_Protein_Analyses.zip:</strong> <strong>CvP_IVYWREL_plots.py: </strong><em>Script used to compare IVYWREL bias to OGT for all genomes after removing transmembrane proteins</em> <strong>concat232SCC.trimaln: </strong><em>Concatenated and trimmed alignment file for the 232 single-copy-core proteins used in all SCC analyses.</em> <strong>concat232SCC.tree: </strong><em>Tree in Newick format reconstructed under a homogenous model; shown on Figure 1</em> <strong>concat232SCC.tree.log: </strong><em>IQ-Tree output log for the SCC tree shown on Figure 1</em> <strong>concat232SCC.trimmedalignment.customDayhoffRecoding.phy: </strong><em>Alignment in Phylip format after recoding using custom-Dayhoff bins</em> <strong>concat232SCC.customDayhoffRecoding.RAxML.tree: </strong><em>Tree in Newick format reconstructed from the custom recoded alignment; shown on Supplementary Figure 7</em> <strong>concat232SCC.PSMF.tree: </strong><em>Tree in Newick format reconstructed under PSMF Model; shown on Supplementary Figure 8</em> <strong>concat232SCC.GHOST.tree: </strong><em>Tree in Newick format reconstructed under GHOST Model; shown on Supplementary Figure 9</em> <strong>recode_sequences.py: </strong><em>Script used for recoding alignment files</em> <br> <strong>Gene_Family_Minimum_Bipartition_Analyses.zip</strong> <strong>compute_MinimumBipartitionsData_fromTrees.py: </strong><em>Script used to compute the minimum bipartitions data from phylogenetic trees</em> <strong>named_trees.zip: </strong><em>Newick-formated trees (leaves with accessions and leaves with names) for orthogroups containing Mesoaciditoga lauensis. </em> <strong>Orthogroup_Sequences.zip: </strong><em>Amino acid sequences of proteins (in FASTA format) for all orthogroups detected in analyzed Thermotogota genomes; only orthogroups including both A. saccharophila and M. lauensis were used in minimum bipartition analyses.</em> <br> <strong>STRING_files.zip</strong> <strong>Network_A folder: </strong>Network on Panel A of Figure 5 <strong>string_functional_annotations.tsv: </strong><em>Functional annotations for each node, including "STRING cluster" categories</em> <strong>string_interactions.tsv: </strong><em>Node interaction information, including interaction strength</em> <strong>string_mapping.tsv: </strong><em>Map of gene accessions to STRING gene identifiers</em> <strong>string_normal_image.png: </strong><em>Image of STRING network before it was edited for Figure 5</em> <br> <strong>Network_B folder: </strong>Network on Panel B of Figure 5 <strong>string_functional_annotations.tsv: </strong><em>Functional annotations for each node, including "STRING cluster" categories</em> <strong>string_interactions.tsv: </strong><em>Node interaction information, including interaction strength</em> <strong>string_normal_image.png: </strong><em>Image of STRING network before it was edited for Figure 5</em>