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. Heatmap representing different categories of Eukaryotic-like proteins (ELPs) from a) P. luteaand b) I. palifera skeletal MAGs. Bar plots represent the total count of ELPs in a MAG. Numbers in the ARP column denote the count of Ankyrin repeat proteins in MAGs which devote >0.2% of total genes to ARPs, suggesting a potentially host-associated lifestyle. Detailed information about these MAGs is available in the Supplementary data file.
3. Figure 3 Heatmap of KEGG-based nitrogen, sulphur and anoxygenic photosynthesis modules in a) P. lutea and b) I. palifera MAGs, with the representation of their taxonomic classes. MAGs with at least one module >75% complete are shown here.
4. Supplementary Data File: Microsoft Excel File with details of all the MAGs recovered in this work.
4. Supplementary Figure S1. Barplots depicting the metagenome bins recovered after each step. Only High-quality bins were used for performing all the analysis.
5. Supplementary Figure S2. Boxplot for P. lutea and I. plaifera MAGs completeness and contamination stats.
6. 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.
4. Misbinned_contig_remover.py: Python script to remove mis-binned contigs from bins.
5. All_commandlines.txt: Details all the steps, software packages and parameters used in this analysis.
6. Bin_stats_plot.R: R script for plottin the barplots shown in Supplementary Figure S1
7. Completeness_contamination_boxplot.R Rscirpt for plotting the box plots shown in Supplementary Figure S2
8. ELPs_sum_host_associated_heatmap.R: Rscript for plotting the heatmap of ELPs recovered from MAGs as shown in Figure 2
9. Heatmap_selective_module.R Rscript for plotting the heatmap of KEGG modules recovered from MAGs as shown in Figure 3
10. Coverage_barplot.R: Rscript for plotting stacked barplots for relative abundance of MAGs as shown in Supplementary Figure S3.