Genomic view of archaeal and bacterial diversity in skeleton of coral Porites lutea and Isopora palifera

This includes all the figures, scripts and command-line parameters used for the analysis presented in the manuscript  Genomic view of archaeal and bacterial diversity in skeleton of coral Porites lutea and Isopora palifera

1. Figure 1. Phylogenetic trees of Metagenome-assembled genomes (MAGs) recovered from P. lutea and I. palifera skeleton. a) 376 bacterial MAGs, with genome completeness, GC content, and genes-of-interest and b) 17 archaeal MAGs with the presence of ammonia oxidising gene AmoA. The phylogenetic tree was constructed using a concatenated alignment of 120 bacterial and 122 archaeal marker genes, respectively. Taxonomic annotation of bacterial MAGs  (counterclockwise): Proteobacteria, Desulfobacterota, DSWW01,Desulfobacteriota_F, Nitrospinota, Bdellovibrionota, Desulfobacterota_B, Myxococcota, SAR324. Bdellovibrionota, Acidibacteriota, Bacteroidota, Calditrichota, SM23-31, AABM5-125-54, Marinosomatota, Zixibacteria, Gemmatimondota, Fibriobacterota, Elusimicrobiota, Omnitrophota, Sumerlaeota, Planctomycetota, Verrucomicrobiota, Chlamydiota, Spirochaetota, Firmicutes_A, Firmicutes, Fimicutes_H, Firmicutes_G, Cyanobacteria, Chloroflexota, Patescibacteria, Actinobacteriota, Bipolaricaulota. 

2. Figure 2. Phylogenetic tree of bacterial MAGs with representation of different categories of Eukaryotic-like proteins (ELPs) from a) P. lutea and b) I. palifera. From inner to outer, Innermost circle represents MAGs color coded at bacterial class level, heatmap represents different ELP categories (Inner to outer: HEAT repeats; WD domain repeats, WD40; Ankyrin Repeats, ARPs; and Tetratricopeptide repeats, TPRs) and Bar plot represent total ELP counts in MAGs. Bars colored in “sky blue” represent MAGs which devote >0.2% of total genes to ARPs, suggesting a potentially host-associated lifestyle.  Detailed information about these MAGs and distribution of ELP protein families is available in the Supplementary data file.

3. Figure 3. Phylogenetic tree of bacterial MAGs representing functional pathways based on nitrogen, sulphur and anoxygenic photosynthesis KEGG modules in a) P. lutea and b) I. palifera. From inner to outer ring, Innermost circle represents MAGs color coded at bacterial class level. Heatmap represents different KEGG modules (from inner to outer) for Nitrogen metabolism (M000175, M00524, M00529, M00530 and M00531), Sulfur metabolism (M00596, M00176 and M00595) and Anoxygenic photosynthesis (M00597). MAGs with at least one KEGG module 100% complete is shown here.

4. Supplementary Data File: Microsoft Excel File with details of all the MAGs recovered in this work. 

5. Supplementary Figure S1. Barplots depicting the metagenome bins recovered after each step. Only High-quality bins were used for performing all the analysis.

6. Supplementary Figure S2. Boxplot for P. lutea and I. plaifera MAGs completeness and contamination stats.

7. Supplementary Figure S3. Stacked barplots for Relative abundance (>1%) of MAGs taxonomic classes for P. lutea and I. palifera.  p_Aenigmatarchaeota, p_Nanoarchaeota, p_Thermoproteota represents the Archaea domain.

8. Supplementary Figure S4. Heatmaps representing bacterial MAGs from a) P. lutea and b) I. palifera with at least one KEGG module >75% complete. MAGs are annotated at Class level.

9. Misbinned_contig_remover.py:  Python script to remove mis-binned contigs from bins. 

10. All_commandlines.txt: Details all the steps, software packages and parameters used in this analysis.

11. Bin_stats_plot.R: R script for plottin the barplots shown in Supplementary Figure S1.

12. Completeness_contamination_boxplot.R Rscirpt for plotting the box plots shown in Supplementary Figure S2.

13. Coverage_barplot.R: Rscript for plotting stacked barplots for relative abundance of MAGs as shown in Supplementary Figure S3.

14. Heatmap_selective_module.R Rscript for plotting the heatmap of KEGG modules recovered from MAGs as shown in Supplementary Figure S4.