Additional file 1 of Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
Creators: name: Tian, Renmao
name: Ning, Daliang
name: He, Zhili
name: Zhang, Ping
name: Spencer, Sarah J.
name: Gao, Shuhong
name: Shi, Weiling
name: Wu, Linwei
name: Zhang, Ya
name: Yang, Yunfeng
name: Adams, Benjamin G.
name: Rocha, Andrea M.
name: Detienne, Brittny L.
name: Lowe, Kenneth A.
name: Joyner, Dominique C.
name: Klingeman, Dawn M.
name: Arkin, Adam P.
name: Fields, Matthew W.
name: Hazen, Terry C.
name: Stahl, David A.
name: Alm, Eric J.
name: Zhou, Jizhong
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Heatmap showing the profile of contaminants in the background (B), low (L), mediate (M) and high (H) contamination wells. The concentrations of each contaminant were scaled linearly [(X-min)/max] to 0-1 for comparison. Figure S2. Maximum Likelihood (ML) tree of well-established bacterial and archaeal phyla, Patescibacteria superphylum and Candidate phyla of this study based on concatenated rp16 genes. Figure S3. Completeness evaluation of genome bins based on CheckM analysis (A) and number of unique tRNA genes (B). Figure S4. Comparison of ribosomal protein genes in the Patescibacteria superphylum and the other phyla. Figure S5. The rarefaction curve of the sequences showing the diversity index of observed OTUs and Shannon. The curves were based on calculation of diversity with step size of 2000 and iteration number of 10. Figure S6 The enrichment of Patescibacteria cells on the 0.2-micron filter in comparison to the 10 or 3 micron filter (showing 108 sample with Patescibacteria abundance &gt;0.5% in 0.2-micron filter). Figure S7. Comparison of transporter proteins in the superphylum Patescibacteria and other phyla. Figure S8. Number of CRISPR proteins (A) and CRISPR spacers (B) in the non-Patescibacteria phyla of Jillian Banfield’s binning. Figure S9. Number of CRISPR proteins (A) and CRISPR spacers (B) in the non-Patescibacteria phyla of this study. Figure S10. A heatmap of comparison of phage-associated proteins including phage structure, phage integration and regulation in the Patescibacteria superphylum and the other phyla. The color indicates the standardized number of phage proteins in each genome / bin.Table S1. Metadata of the ground water samples. See Figure S1 for the contaminant concentrations and the categorization of wells. Table S2. Summary of the raw reads and qualified reads of the metagenomic data. Table S3. Metagenomic assembly of the samples plus supplementary sequence. Contigs with length &gt;500 bp were summarized. * The assembly of the sample FW301-10 failed due to super large data size and high diversity of community. Table S4. The alignment rates of each sample’s reads to its assembly. The alignment rates were calculated by Bowtie2 and Samtools. Table S5. Profiles of genome bins generated by MetaBat. Only genome bins with completeness &gt;70% and contamination &lt;10% are listed. Table S6. Genome sizes of Patescibacteria and non-Patescibacteria members including well-established phyla, newly defined phyla and genome bins of this study.