Additional file 3 of Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR

Additional file 3: Supplementary Table 1. Sampling details for the analysed metagenomes. Supplementary Table 2. Completeness of MAGs calculated based on 43 SCGs (Anantharaman, Brown, Hug, et al. 2016). Supplementary Table 3. Basic statistics and taxonomy (GTDB, NCBI) for the MAGs assembled in this study. Supplementary Table 4. List of final, dereplicated bins and the ones of lower quatily that were collapsed into them. Supplementary Table 5. Annotation results of CPRs at class level. KEGG modules were manually checked for completeness after annotationg the bins using different databases (Panda, TIGR, COG, Interproscan and Pfam). Supplementary Table 6. Recruitment results (coverage per Gbp) for all bins versus all samples analyzed in this study. Supplementary Table 7. Basic statistics for Refseq 81 database, representative CPR genomes from GTDB r89 and the MAGs assembled in this study. Supplementary Table 8. Basic statistics for the manually curated SPC database used in this study. Supplementary Table 9. Basic statistics for the manually curated free-living bacteria database used in this study. Supplementary Table 10. Basic statistics for the representative CPRs genomes in GTDB versions r89 database. Supplementary Table 11. List of CPR FISH probes (their sequence, specificity and target group) and cells measurements and statistics. Supplementary Table 12. Average nucleotide identity (ANI) values computed between all pairs of freshwater CPR MAGs obtained in this study. Supplementary Table 13. GRiD results for the dereplicated bins, estimating the rate of genome replication. Supplementary Table 14. Phage defense systems and their occurencess in CPRs, SPCs and free-living bacteria. Supplementary Table 15. Predicted rhodopsins in CPRs, including all GTDB representative genomes and the282 MAGs obtained in this study. Supplementary Table S16. CAZys and their occurence in freshwater CPR genomes.