Additional file 2 of Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups
Creators: name: Méheust, Raphaël
name: Castelle, Cindy J.
name: Jaffe, Alexander L.
name: Banfield, Jillian F.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Taxonomic assessment and distribution of the 1,179 representative genomes. Maximum-likelihood phylogeny based on a 14-ribosomal-protein concatenated alignment (2,388 positions) using the LG plus gamma model of evolution. Scale bar indicates the average substitutions per site. Figure S2. The protein clustering pipeline used in the study. MAGs: metagenome-assembled Genomes. Figure S3. Quality assessment of the protein clustering. A. Consistency between the KEGG annotations and the protein families. For each of the 6482 annotations, we reported the family which contains the highest percentage of protein members annotated with that KEGG annotation. Each dot represents a KEGG annotation, the y-axis represents the highest percentage. C. Contamination of the protein families. For each family with proteins having KEGG annotations, we computed the percentage of the proteins that have KEGG annotations different than the most abundant one, this percentage defined the annotation admixture (y-axis). Each dot represents a protein family. Figure S4. Comparison between the protein clustering performed in this study and the Unifam and the arCOG databases. The Venn diagram shows the number of ORFs within the 1,179 genomes that were clustered into families defined in this study (purple) and that have hits with arCOG (green) and Unifam (yellow) HMMs. Figure S5. Correlation plot of 4 trees obtained from 3 different hierarchical clustering methods (complete linkage, average linkage and single linkage). Maximum-likelihood tree based on RAxML is also shown (“Phylogenetic tree”). Correlations are based on cophenetic distance matrices between pairs of trees. Positive correlations are displayed in blue and negative correlations in red color. Color intensity is proportional to the correlation coefficient. Figure S6. The distribution of 10,866 widely distributed protein families (columns) in 1,179 representative genomes (rows) from Archaea. The families of the 19 modules discussed in the study were colored. Data are clustered based on the presence (black) and absence (white) profiles (Jaccard distance, complete linkage). Figure S7. Number of genomes per family in 14 selected modules. X-axis represents the families and y-axis the number of genomes. For each family, the number of genomes of Methanomicrobia, Methanobacteria, Halobacteria, Crenarchaeota, Poseidoniales (Marine group II), Thermococci, Archaeoglobi, Thaumarchaeota, Thermoplasmata and Methanomassiliicoccales are shown by a colored dot. Figure S8. Presence and absence of 37 families of modules 65, 72, 129 and 184 in genomes of methanogen archaea. Scale bar indicates the average substitutions per site. Figure S9. Presence and absence of 11 families of modules 32, 45, 71, 135 in the genomes of Poseidoniales. Scale bar indicates the average substitutions per site. Figure S10. Presence and absence of 15 families of modules 2 and 66 in genomes of Crenarchaeota. Scale bar indicates the average substitutions per site. Figure S11. Presence and absence of 4 families of module 142 in genomes of Thaumarchaeota. Scale bar indicates the average substitutions per site. Figure S12. Presence and absence of 14 families of module 8 in genomes of Thermococci. Scale bar indicates the average substitutions per site. Figure S13. Presence and absence of 11 families of modules 13 and 108 in genomes of Halobacteria. Scale bar indicates the average substitutions per site. Figure S14. Presence and absence of 6 families of module 48 in genomes of Asgard. Scale bar indicates the average substitutions per site. Figure S15. The length distribution of hypothetical proteins (in amino acid).