Additional file 1 of Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments
Creators: name: Zhang, Zhi-Feng
name: Liu, Li-Rui
name: Pan, Yue-Ping
name: Pan, Jie
name: Li, Meng
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1: Supplementary materials. Results of community structure and metabolic profiles of microbial community in mangrove sediment. And the taxonomic description of new candidate phylum Candidatus Cosmopoliota. Fig. S1. Statistics of MAGs derived from Illumina assembly, PacBio assembly, and Hybrid assembly. (a) The number and percentage of MAGs under different quality strategies. (b) The Venn diagram shows the distribution of refined MAGs from each assembly. Fig. S2. Comparison of draft MAGs derived from Illumina assembly, PacBio assembly, and Hybrid assembly. (a) Comparison of the longest contig and contig number in each draft MAGs derived from three assemblies. (b) Comparison of N50 and contig number in each draft MAGs derived from three assemblies. Fig. S3. Average amino acid identity (AAI) comparison of draft MAGs for 12 refined high-quality MAGs. Each of these 12 refined high-quality MAGs have three high-quality (CheckM-completeness ≥ 90%, CheckM-contamination &lt; 5%) and high fastANI similarity (&gt; 99%) draft MAGs derived from three assemblies (Illumina assembly, PacBio assembly, and Hybrid assembly), respectively. Fig. S4. Collinearity analyses of draft MAGs for 12 refined high-quality MAGs. Each of these 12 refined high-quality MAGs have three high-quality (CheckM-completeness ≥ 90%, CheckM-contamination &lt; 5%) and high fastANI similarity (&gt; 99%) draft MAGs derived from three assemblies (Illumina assembly, PacBio assembly, and Hybrid assembly), respectively. (a) Genome collinearity of three draft MAGs of each refined MAGs; “Ill” in x-axis represents Illumina, “Hyb” represents Hybrid, and “Pac” represents PacBio; The parts of forward collinearity are displayed in blue color, these of reverse collinearity is in green, and the unmatched regions are in red color. (b) Gene collinearity of three draft MAGs of each refined MAGs; The three long strips consisted of couples of short strips in each subgraph represent three draft MAGs derived from Illumina assembly, Hybrid assembly, and PacBio assembly, respectively; each short strip in long strip represents one contig of the draft MAG; The gray bands connecting two draft MAGs represent the collinearity relationship (&gt; 20 genes) between the genes in two draft MAGs. Fig. S5. Genomic collinearity of draft MAGs for 12 refined high-quality MAGs. Each of these 12 refined high-quality MAGs have three high-quality (CheckM-completeness ≥ 90%, CheckM-contamination &lt; 5%) and high fastANI similarity (&gt; 99%) draft MAGs derived from each of three assemblies (Illumina assembly, PacBio assembly, and Hybrid assembly), respectively. The green lines in the graphic are the separation of adjacent contig, which are corresponding to the up x-axis and right y-axis, respectively. While, the bottom x-axis and left y-axis represent the genome location. Fig. S6. Gene collinearity of draft MAGs for 12 refined high-quality MAGs. Each of these 12 refined high-quality MAGs have three high-quality (CheckM-completeness ≥ 90%, CheckM-contamination &lt; 5%) and high fastANI similarity (&gt; 99%) draft MAGs derived from each of three assemblies (Illumina assembly, PacBio assembly, and Hybrid assembly), respectively. The green lines in the graphic are the separation of adjacent contig, which are corresponding to the up x-axis and right y-axis, respectively. While, the bottom x-axis and left y-axis represent the genome location. Fig. S7. Relative abundance of microbial community and specific genes in different sediment depth. (a) Composition of Prokaryotes, Eukaryotes, Archaea, Bacteria, and Fungi based on 16S rRNA and ITS genes against SILVA database and UNITE database for all eukaryotes, respectively. (b) Composition of Hydrogenases, [NiFe]-Hydrogenases, [FeFe]-Hydrogenases, Carbohydrate-Active Enzymes (CAZymes), and dissimilatory sulfite reductase (dsr) genes. Fig. S8. Read count of microbial community and specific genes in different sediment depth. Read counts are standardized to CPM (count (read) per million reads). (a) Read count of Prokaryotes, Eukaryotes, Archaea, Bacteria, and Fungi based on 16S rRNA and ITS genes against SILVA database and UNITE database for all eukaryotes, respectively. (b) Read count of Hydrogenases, [NiFe]-Hydrogenases, [FeFe]-Hydrogenases, Carbohydrate-Active Enzymes (CAZymes), and dissimilatory sulfite reductase (dsr) genes. Fig. S9. Read count of metagenomic reads for specific genes in different sediment depth. Read counts are standardized to CPM (count (read) per million reads). Abbreviation: NiFe/FeFe, [NiFe]-/[FeFe]-hydrogenases; atpA, ATP synthase; coxA, cytochrome c oxidase; cyoA, cytochrome o ubiquinol oxidase; ccoN, cytochrome c oxidase; HCO, haem-copper oxidase genes (coxA, cyoA and ccoN); cydA, cytochrome bd oxidase; acsB, acetyl-CoA synthase; mcrA, methyl-CoM reductase; dsr, dissimilatory sulfite reductase; sor, sulfur oxygenase/reductase; narG, dissimilatory nitrate reductase; napA, periplasmic nitrate reductase; nir, dissimilatory nitrite reductase; nrf, ammonifying nitrite reductase; nif, nitrogenase; nifH, nitrogenase iron protein; rbcL, ribulose 1,5-bisphosphate carboxylase; pfor, pyruvate-ferredoxin oxidoreductase. Fig. S10. Glycoside hydrolases (GH) identified by CAZy searches of the MAGs. GH families that contain enzymes that are not specifically involved in degradation were specifically identified by Pfam or EC numbers in the annotations, based on Wrighton et al. 2014. Fig. S11. Pathway completeness of all refined MAGs calculated by KEGGDecoder. The pathway completeness is defined as the percentage of core genes of specific pathways identified in each MAG. Complete lists of metabolic genes or pathways can be found in Dataset S2 Sheet7. Detailed gene lists for each pathway indicated can be found at: https://github.com/bjtully/BioData/blob/master/KEGGDecoder/KOALA_definitions.txt . The up row of heatmap shows the MAG completeness, and the bottom raw represent the phylogenetic information of each MAG at phylum level (Archaea in purple and Bacteria in blue). Fig. S12. The phylogenetic tree of Candidatus Cosmopoliota and the adjacent phyla based on 16S rRNA genes. The genomes of Ca. Cosmopoliota are labeled in orange color and bold font. Fig. S13. The average amino acid identity (AAI) values between each genome in Candidatus Cosmopoliota and the adjacent phyla. The genomes of Ca. Cosmopoliota are labeled in orange color and bold font. Fig. S14. The average nucleotide identity (ANI) values between the 16S rRNA genes of Ca. Cosmopoliota and the adjacent phyla. The genomes of Ca. Cosmopoliota are labeled in orange color and bold font.