Methods to make 16S rRNA gene tree of Bathyarchaeota and intermediate files
Files
- Original fasta: CKY_BS90_kgf.de.fasta
- Trimmed alignment: CKY_BS90_kgf.de.sina.trim5.fasta
- Tree file: S-6WHuekat59NLLehFrMWA_newick.txt.mdf
- Assignment of subgroup: sseqs_subgroup.txt
Methods to make 16S rRNA gene tree of Bathyarchaeota
16S rRNA gene sequences were collected from SILVA SSU database version 128 (sequences of Bathyarchaeota and Group C3; > 750bp) and Xiang’s Peatland MCG sequences (Xiang et al. 2017), all sequences were clustered at 90% identity using Usearch v10.0.240 (https://www.drive5.com/usearch/), then 16S rRNA gene sequences from available Bathyarchaeota genomes in public database, anchor sequences from Kubo et al. and outgroup sequences of Crenarchaeota, YNPFFA group and Korarchaeota were added (Kubo et al. 2012). All sequences were aligned using SINA v1.2.11 (vision 21227) with SSU arb database version 128, and poor aligned columns (gaps in 50% or more of the sequences) were deleted by using trimAl v1.4.rev15 (Capella-Gutiérrez et al. 2009; Ludwig et al. 2004; Pruesse et al. 2012). Phylogenetic analyses of 16S rRNA sequences were inferred by Maximum Likelihood implemented in RAxML 8.0 on The CIPRES Science Gateway using the GTR+GAMMA model and RAxML halted bootstrapping automatically (Miller et al. 2010; Stamatakis 2014).
Reference:
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Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic treesGateway Computing Environments Workshop (GCE), 2010: IEEE, 2010, 1-8.
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Xiang X, Wang R, Wang H et al. Distribution of Bathyarchaeota Communities Across Different Terrestrial Settings and Their Potential Ecological Functions. Sci Rep 2017;7: 45028.