Main and Supplementary Tables and Figures

2017-04-22T22:17:23Z (GMT) by A. Murat Eren
Main and Supplementary Tables and Figures in Delmont et al.<div><br></div><div>---</div><div><br></div><div>Figure 1: Geographically bounded metagenomic co-assemblies. Dots in the map correspond to the geographic location of 93 metagenomes from the TARA Oceans project. Each dot is associated with a metagenomic set (corresponding to a geographic region) for which we performed a metagenomic co-assembly (n=12). The number of metagenome-assembled genomes (MAGs) we characterized from each metagenomic set varied from 13 to 141 after the removal of redundant MAGs, for a total of 957 non-redundant MAGs encompassing the three domains of life.</div><div><br></div><div>Figure 2: Nexus between phylogeny and function of HBDs. (A) genomic feature summary of the nine HBDs. (B) Phylogenomic analysis of 432 Proteobacteria MAGs and 43 Planctomycetes MAGs in the non-redundant genomic database (including the nine HBDs) using a collection of 37 phylogenetic marker gene families. Layers surrounding the phylogenomic tree indicate genome size and taxonomy of each MAG at the phylum and class level. (C) Functional network of the nine HBDs base upon a total of 5,912 identified gene functions. Size and colour of genomic nodes represent the number of detected functions and MAG taxonomy, respectively. Finally, the colour of functional nodes indicates their occurrence in the different HBDs.</div><div><br></div><div>Figure 3: Phylogeny of nitrogen fixation genes. Phylogenetic analysis of nifD (A) and nifH (B) occurring in the 15 nitrogen fixing MAGs (including five redundant MAGs) we identified from TARA Oceans in relation to 252 and 316 reference genomes, respectively. MAGs are colored based on their phylogenetic affiliation at the phylum level.</div><div><br></div><div>Figure 4: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean. Cumulative relative distribution of the Planctomycetes (n=2) and Proteobacteria (n=7) HBDs in 93 metagenomes corresponding to 12 marine geographic regions (box-plots), and niche partitioning of HBD-06, HBD-07, HBD-08 and HBD-09 at the surface of four oceans and two seas (61 metagenomes from surface samples, world maps). *Assuming that each litre in the surface ocean contains 0.5 billion archaeal and bacterial cells.<br><div><br></div><div><div>Figure S1: Phylogenetic analysis of nifH genes. The figure describes nifH genes in 15 nitrogen fixing MAGs (including five redundant MAGs) and nine orphan scaffolds we identified in this study, as well as 504 reference genomes. </div><div><br></div><div>Table S1: The summary of the 93 metagenomes from TARA Oceans, and the twelve geographic regions they represent.</div><div><br></div><div>Table S2: The summary of the co-assembly and binning outputs for each metagenomic set.</div><div><br></div><div>Table S3: Genomic features of 957 MAGs from the non-redundant genomic database. The table includes the mean coverage, relative distribution, detection and number of recruited reads for each MAG across the 93 metagenomes. It also includes specific metadata for MAGs (including five redundant MAGs) corresponding to the nine HBDs. Finally, the table describes the gene-level detection of HBD-06 and HBD-09 across the 93 metagenomes. </div><div><br></div><div>Table S4: The 16S rRNA gene sequence identified in HBD-09.</div><div><br></div><div>Table S5: Genomic features, Pearson correlation (based on the relative distribution in 93 metagenomes) and average nucleotide identity of 1,077 MAGs from the redundant genomic database.</div><div><br></div><div>Table S6: RAST subsystems and KEGG modules for the nine HBDs .</div><div><br></div><div>Table S7: nifH gene sequences in MAGs, orphan scaffolds, as well as the reference sequence γ-24774A11, along with their mean coverage across the 93 metagenomes.</div><div><br></div><div>Table S8: Genomic features of 30,244 bins manually characterized from the 12 metagenomic sets. Completion and redundancy estimates are based on the average of four bacterial single-copy gene collections.</div><div><br></div><div>Table S9: KEGG annotation for 1,077 MAGs.</div><div><br></div><div>Table S10: Relative distribution of 1,077 MAGs across the 93 metagenomes.</div><div><br></div></div></div>