Additional file 2 of Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota

Supplementary Material 2: Tables S1. ASV counts and relative abundances of archaeal 16S rRNA gene amplicon sequencing for control and protein amended samples. S2. Top hits of a megablast search of the Ca. Penumbrarchaeia ASV sq2 and 16S rRNA gene obtained from the Ca. Penumbrarchaeia MAG E3_1_d157 against the rRNA/ITS database of the NCBI RefSeq Targeted Loci Project. S3. Overview list of metagenomic studies, in which Ca. Penumbrarchaeia MAGs had a coverage > 2. These studies were used to reconstruct Ca. Penumbrarchaeia MAGs. S4. Overview list of MAGs obtained in this studyS4. Overview list of MAGs obtained in this study. S5. Quality statistics computed with checkM and checkM2 and taxonomy information computed using gtdb_tk with the GTDB database v207S5. Quality statistics computed with checkM and checkM2 and taxonomy information computed using gtdb_tk with the GTDB database v207. S6. Table containing relative abundances of single MAGs in mapped metagenomic runs. S7. List of all unique metagenomic runs, in which Ca. Penumbrarchaeia MAGs were found with meta data derived from ENA of the sampling location and environment details. . S8. List of Orthogroups, which were selected as core genome (Orthogroup present in at least 90% of MAGs). The table shows gene counts for each MAG within single orthogroups. S9. Gene counts for single pathways within each of the Ca. Penumbrarchaeia MAGs. Genes were extracted from the core genome and annotated using NR and kegg. Based on found annotations genes were grouped into kegg pathway descriptions. S10. Full annotation of genes, which were found in all orthogroups of the core genome. Annotation was performed using kegg, NR, OM_RGC, dbCAN and merops. S11. Full annotation of selected pathways for all 35 Ca. Penumbrarchaeia MAGs. Annotation was performed using KEGG (release 104) and NR (release 13/05/2023), dbCAN (v3.0.7) and merops (v12.4). S12. Annotation of peptidases found in all 35 Ca. Penumbrarchaeia MAGs. The annotation was performed using merops (v12.4). S13. Annotation of CAZymes found in all 35 Ca. Penumbrarchaeia MAGs. The annotation was performed using dbCAN (v3.0.7). Results were validated with NR and KEGG annotations.S14. Gene counts for the categories annotated, hypothetical and unknown, along with percentages for each category. S15. Counts of rarity groups per habitat. S16.Overview table of all Thermoplasmatota MAGs with their taxonomic classification, fraction of occurrence, percentage of unknown genes (perentage_unknown), rarity and habitat. S17. Studies from selected marine metagenomics literature and matched with BioProject identifiers from the European Nucleotide Archive for MAG reconstruction in OMDv2