0000000000394675
AUTHOR
Alberto Torcello-requena
Additional file 12 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 12: Fig. S3. Genomic context of the phoBR two-component system in different marine, brackish and freshwater cluster 5 picocyanobacteria. Each subunit is color coded accordingly. The right panel shows a phylogenomic tree with all those freshwater strains (colored red) possessing two copies of the phoB gene.
Additional file 20 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 20: Fig. S5. Total number (Y axis) of A) transposases and B) integrases found in freshwater, brackish and marine picocyanobacteria.
Additional file 18 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 18: Fig. S4. Phylogenetic analysis of picocyanobacterial Ni/Cu/Zn/Fe/Mn superoxide dismutases. The Ni-type maturation protease from marine strains was used to root the tree. Bootstrap values >75 are shown and the habitat of each picocyanobacterial enzyme is color coded.
Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Abstract Background Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. …
Additional file 2 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 2: Fig. S1. Average Nucleotide Identity (ANI) matrix between all 132 compared picocyanobacteria from SCs 5.1, 5.2 and 5.3.
Additional file 4 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 4: Fig. S2. A) Cross-comparison of strict core, soft core, shell and cloud in all 132 picocyanobacteria from all habitats and SCs. B) Plots estimating the core genome (n° of genes) and pangenome (n° of genes) of all three SCs. C) Functionality of the meta-pangenome of picocyanobacteria assessed by SEED/KEGG. Each gene category is color coded for the shared (strict core, soft core) and flexible (shell and cloud) genome.
Additional file 6 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 6: Additional Dataset 3. 5.1-5.2-5.3 meta-pangenome. Core, strict-core, shell and cloud annotated genes with Cyanorak clusters (CK) and SEED.
Additional file 15 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 15: Table S8. Compatible solutes and osmolytes. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 8 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 8: Additional Dataset 4. Non-clustered CK genes from all 132 analyzed picocyanobacteria. BLASTP results obtained with the closest taxon from the NCBI nr database.
Additional file 16 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 16: Table S9. Broad transporters, permeases, channels and uptake systems. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 21 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 21: Table S12. Mobile genetic elements. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 5 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 5: Additional Dataset 2. Pangenomic analysis between all picocyanobacterial isolates from SCs 5.1, 5.2 and 5.3. The total number of genes for each category (strict core, soft core, shell and cloud) and isolate are specified.
Additional file 11 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 11: Table S5. P metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 3 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 3: Additional Dataset 1. Average and standard deviation genome size, median intergenic spacers, coding density and %GC of all culture-derived picocyanobacteria. Single pair ANOVA tests for each origin and sub-cluster and for different genomic features.
Additional file 1 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 1: Table S1. Main genomic features of marine, brackish and freswhater culture-derived picocyanobacteria. An asterisk in the origin column indicates strains where euryhaline physiology is known.
Additional file 14 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 14: Table S7. Amino acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 10 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 10: Table S4. N metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 19 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 19: Table S11. Reactive oxygen species (ROS). Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 13 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 13: Table S6. C fixation/photosynthesis. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 9 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 9: Table S3. S metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 17 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 17: Table S10. Glycerolipid/Fatty acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 7 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 7: Table S2. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters.