DOI: 10.6084/m9.figshare.15088110
title: Adam, Kolyfetis et al., 2022. Supplementary Data.

description: Compressed Supplementary Data files for (Adam, Kolyfetis, et al., 2022). File descriptions are given below and in more detail in the readme file. This is version 20220819. <br> Data_S1 Data regarding all DUF phylogenies (taxonomic distributions, HMM profiles, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, phylogeny runs), plus lists of genomes in local databases. <br> Data_S2 Data regarding methanogenesis markers phylogenies from (Borrel et al., 2019) (HMM profiles, DIAMOND query sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs). <br> Data_S3 Data regarding methanogenesis marker phylogenies from (Gao & Gupta, 2007) and phylogenies of Wood-Ljungdahl pathway and methyltransferase proteins (HMM profiles, DIAMOND query sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs), plus SyntTax outputs. <br> Data_S4 Data regarding congruence tests and the concatenation phylogeny of Mcr. <br> Data_S5 Data regarding congruence tests and the concatenation phylogeny of Mtr. <br> Data_S6 Data regarding phylogenies of additional Eha, Ehb and Hcg proteins (HMM profiles, DIAMOND query sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs). <br> Data_S7 Data regarding congruence tests and the concatenation phylogeny of Eha. <br> Data_S8 Data regarding congruence tests and the concatenation phylogenies of Ehb. <br> Data_S9 Data regarding all rooting analyses on the concatenations and the methyltransferases genes. <br> Data_S10 Data regarding gene and site concordance factor calculations for all concatenations. <br> Data_S11 Data regarding all Ancestral Sequence Reconstruction runs, homology searches of the ancestral sequences, trimmed ancestral sequences, and homology modeling of McrA. <br> Data_S12 Data regarding congruence tests and the concatenation phylogenies of the Hcg proteins. <br> Data_S13 Data regarding site-specific rate calculations, benchmarks, and all related statistical tests. Transmembrane segment prediction runs and statistical tests for their relationship eith site-specific rates. <br> Data_S14 Data regarding the phylogenetic runs for the taxonomic placement of NRA7 (Archaeoglobi) and Bathyarchaeia metagenomic bins. Also data regarding AAI/ANI, biogeography, and 16S analyses, plus CheckM outfiles. <br> Data_S15 Data regarding the results of the metabolic prediction (BlastKOALA/dbCAN2/HydDB/MEROPS) for the genomes studied. <br> Data_S16 Custom scripts (same as in the manuscript's Github repository, along with their license and readme file) and a file with the R functions (statistics) used in the analyses. <br> Changelog v5 (20220819) 1) Added Data_S16 (customs scripts, R functions). 2) Changed title to correspond to expected publication year for the manuscript, instead of the preprint. <br> Changelog v4 (20220424) 1) Added the SyntTax csv outputs to Data_S3. <br> Changelog v3 (20220422) 1) Added the names-assemblies files (lists of genomes) in Data_S1. 2) Changed filenames from "Supplementary_Data_<em>N</em>" to "Data_S<em>N</em>". <br> Changelog v2 (20220411) 1) Numbering of Supplementary Data files changed to corrrespond to the revised manuscript. 2) Added MtsB phylogenetic analyses (Data_S3) and rooting (Data_S9). 3) Added taxonomic analyses (Data_S14) and metabolic predictions (Data_S15) for Hydrothermarchaeota and Geothermarchaeales. 4) Added phylogenetic analyses combining the large catalytic subunits of [NiFe] hydrogenase groups 4h (Eha) and 4i (Ehb) (Data_S6). 5) Added Pearson and updated Spearman correlations for rate calculation benchmarks (Data_S13). Added Spearman correlations for desaturation dataset benchmarks (Data_S14).