DOI: 10.6084/m9.figshare.26942083.v1
title: Repository with all analyses described in our paper: The recovery of over 20,000 genomes revealed the diversity, function, and community assembly of hot spring microbiome through metagenomic-centric microbial ecology.Please cite this work if it can be apply to your study.

description: Supplementary Information for "<b>The recovery of over 20,000 genomes </b><b>revealed the diversity, function, and community assembly of hot spring microbiome through metagenomic-centric microbial ecology</b>", including Figure 1-6, Figure S1-S16 and Table S1-S20, original data, and scripts. Below are the concrete descriptions of all files.Files in "<b>1. Figures and Tables</b>" include all the main and supplementary figures of this manuscriptFigure 1: Metagenomic genome reconstruction of geothermal springs in YunnanFigure 2: Community composition and functional profiles of 152 samplesFigure 3: Relationship between environmental variables and species and functional compositionFigure 4: Co-occurrence microbial networks of three geothermal spring groupsFigure 5: Scheme describing the key metabolic pathwaysFigure 6: The relative importance of different ecological processes in three geothermal spring groupsFig. S1: The pipeline of metagenomic and ecological analyses in this studyFig. S2: Sample sites of geothermal springs in Tengchong, Yunnan, ChinaFig. S3: The basic genomic information of all high-quality and medium-quality genomesFig. S4: PCoA of all RMAGs, archaea, bacteria, and KOs in different years based on Bray–Curtis distancesFig. S5: Redundancy analysis (RDA) of the relationship between the environmental variables and the microbial community compositionFig. S6: Analysis of similarity (ANOSIM) plot of pairwise of AG, HG, and TGFig. S7: Principal component analysis (PCA) of environmental variables of Fig. S1Fig. S8: Boxplot of alpha diversity of different sites and groupsFig. S9: Boxplot of functional diversity of different sites and groupsFig. S10: Unique and core species of the three groupsFig. S11: Metabolic category of accessory gene families of three habitatsFig. S12: Co-occurrence functional networks of AGFig. S13: Co-occurrence functional networks of HGFig. S14: Co-occurrence functional networks of TGFig. S15: Heatmap of Zi and Pi values of different phyla in each moduleFig. S16: SNB scores at different taxonomic ranksFiles in "<b>2. Phylogenetic tree</b>" include phylogenetic trees of archaea and bacteria in Fig. 1b, and the universal tree of 31 markers used for iCamp analyses1.gtdbtk.ar53.user_msa.automated1.treefile: tree of archaea based on 53 conserved GTDB archaea markers2.gtdbtk.bac120.user_msa.automated1.treefile: tree of bacteria based on 122 conserved GTDB bacteria markers3.31marker_changename.treefile: tree of both archaea and bacteria used for community assembly processes analyses in iCampFiles in "<b>3. Commands_and_scripts</b>" include R codes and associated input files used in this study1. The relative abundance of 3176 RMAGs in 152 samples2. The taxonomy of 3176 RMAGs3. The summed relative abundance of all archaea classes in 152 samples4. The summed relative abundance of all bacterial phyla in 152 samples5. The relative abundance of KEGG standard categories (level B) in all samples6. The relative abundance of 3176 RMAGs in all samples for PCoA analysis7. The relative abundance of KOs in 152 samples8. The environmental characters of 89 samples used for RDA analysis9. The relative abundance of 3176 RMAGs in 89 samples used for RDA analysis10.31.marker.arc.bac.treefile: tree of both archaea and bacteria used for community assembly processes analyses in iCamp11.Group.csv: Grouping of all sites and samples in this study12.Rcode.R: all the R codes used in this study<br>