DOI: 10.6084/m9.figshare.7154813.v2
title: Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Offers Insight into Ecological Patterns - BiorXiv Submission October 2018

description: Supplemental Data accompanying manuscript analyzing 250 MGII genomes. Includes FASTA files of genomic contigs, proteins, and Anvi'o databases for re-examining manually refined genomes.<br>Supplemental Table 1. Information for all genomes used in study, including source ID numbers, clade and subclade assignment, completion stats (length, percent complete, percent contamination, percent strain heterogeneity), and source reference.Supplemental Table 2. Counts of the number of proteins identified as an extracellular peptidase or carbohydrate-active enzyme for each genome.Supplemental Table 3. A breakdown of the peptidases from the MEROPS database with corresponding IDs and Pfams.Supplemental Table 4. All genomes with identified archaeal flagellum components, including the number of identified components and a prediction of if a full operon is present. Genomes from Tully et al. (2018) used to visualize the putative operon have NCBI contig accession and operon protein IDs listed.Supplemental Table 5. Protein clusters generated using the Anvi’o pangenome workflow identified as either ‘Core MGII’, ‘Core MGIIa’, or ‘Core MGIIb’. Only includes proteins with putative KEGG assignments. Supplemental Table 6. Corresponding metadata (environmental parameters) for Tara Oceans and Ocean Sampling Day samples.<br>Supplemental Data 1. Groups of MGII genomes with ≥98.5% ANI denoting representative and duplicate genome IDs.Supplemental Data 2. Spreadsheet of the pairwise ANI and AAI values for MGIIa and MGIIb.Supplemental Data 3. FASTA format of the 120 marker proteins for all MGII genomes.Supplemental Data 4. Newick file of the phylogenomic tree generated using 120 concatenated marker proteins for the full redundant set of MGII genomes with ≥60 markers. Corresponds to Supplemental Figure 1.Supplemental Data 5. Newick file of the phylogenomic tree generated using 120 concatenated marker proteins for the analyzed set of MGII genomes. Corresponds to Figure 1.Supplemental Data 6. FASTA format of the 16S rRNA gene sequences present in the MGII genomes.Supplemental Data 7. Newick file of the phylogenetic tree generated using the 16S rRNA gene sequences present in the MGII genomes. Corresponds to Supplemental Figure 4.Supplemental Data 8. Pfam HMMs used to identify MEROPS peptidases. The link between Pfams and MEROPS can be found in Supplemental Table 4.Supplemental Data 9. FASTA format of the putative proteorhodopsin sequences identified in the MGII genomes.Supplemental Data 10. Newick file of the phylogenetic tree generated using the proteorhodopsin sequences present in the MGII genomes. Corresponds to Supplemental Figure 6.Supplemental Data 11. GenBank files gathered from NCBI for the putative archaeal flagellum operon for Tully et al. (2018) genomes.Supplemental Data 12. Raw read counts for all MGII contigs generated from Tara Oceans and Ocean Sampling Day samples.Supplemental Data 13. Derived relative fraction and RPKM values for all MGII genomes for all Tara Oceans and Ocean Sampling Day samples. Corresponds to Figure 5 and Supplemental Figure 8.Supplemental Data 14. Spreadsheet of the PERMANOVA statistics (F statistic, p-value, and p-value Benjamini-Hochberg False Discovery Rate) and the results of the ad hoc pairwise PERMANOVA tests (p-value Bonferroni corrected).