DOI: 10.5281/zenodo.5131685
title: Data collection for Tsuji et al., 2020, Type I photosynthetic reaction center in an anoxygenic phototrophic member of the Chloroflexota

description: Supplementary data files associated with Tsuji et al., 2021, "Type I photosynthetic reaction center in an anoxygenic phototrophic member of the<em> Chloroflexota</em>". These files are used by code in a corresponding GitHub repository (https://github.com/jmtsuji/Ca-Chlorohelix-allophototropha-RCI) that shows how various analyses that are presented in the paper were conducted. Files included: Capt_S15_sequencer_data_raw.tar.gz -- Gzipped tarball containing the raw Illumina MiSeq output data for the '<em>Candidatus </em>Chlorohelix allophototropha' subculture 15 sequencing run. The run represents a read cloud sequencing run relying on TELL-Seq technology. Indices can be parsed directly from raw output data using the Tell-Read pipeline. scaffold.full.fasta.gz -- the assembled scaffolds generated using Tell-Read and Tell-Link on the above raw MiSeq output data. Ca_Chx_allophototropha_L227-S17_prokka_ORFs.faa.gz and Ca_Chloroheliaceae_bin_L227_5C_prokka_ORFs.faa.gz -- predicted open reading frames (ORFs) from the curated genomes of '<em>Candidatus </em>Chlorohelix allophototropha' and '<em>Candidatus </em>Chloroheliales bin L227-5C', respectively. These ORFs were predicted using prokka and were used for the analyses presented in the paper. They are similar to, but differ somewhat from, the ORFs predicted by the NCBI gene annotation pipeline that was used upon uploading the genomes to the NCBI Genbank database. Thus, these original ORF files are provided for reference in case comparison is ever needed to the publicly accessible Genbank files. I_TASSER_homology_models_full_output.tar.gz -- Gzipped tarball containing the full output from I-TASSER for homology models of key phototrophy-related genes encoded by '<em>Candidatus </em>Chlorohelix allophototropha' and '<em>Candidatus </em>Chloroheliales bin L227-5C'. After unpacking the tarball, view a summary of the I-TASSER output for each gene by clicking on the 'index.html' file in that gene's folder. lake_survey_MAGs.tar.gz -- Gzipped tarball containing the full collection of 756 metagenome-assembled genomes (MAGs) recovered from the Boreal Shield lake survey, corresponding to those mentioned in Supplementary Data 3. The FastA nucleotide genome sequences, FastA nucleotide predicted protein-coding gene sequences, FastA amino acid predicted protein sequences, and Genome Flat Files (GFFs) for all genomes are provided in the fna, ffn, faa, and gff subdirectories, respectively. lake_survey_MAGs_eggnog_annotations.tar.gz -- Gzipped tarball containing annotations (produced via EggNOG) for all predicted proteins among the 756 MAGs recovered from lake metagenome data. Because proteins were pre-clustered prior to annotation, a "orf2gene" file inside the tarball maps the gene clusters to the ORF IDs used for each genome. lake_survey_MAGs_featureCounts.tsv.gz -- GZipped tab-separated table containing the mapping statistics of metatranscriptome reads on all protein-coding genes from the 756 MAGs recovered from lake metagenome data. lake_survey_Ca_Chloroheliales_MAGs_info.tar.gz -- A subset of information from the previous three files specific to genome bins ELA319 and ELA729, which represent RCI-encoding "<em>Ca</em>. Chloroheliales" members.
description: Changelog: - v1.0.0: First version - v1.0.1: Added uncurated genome bin files - v2.0.0: Added environmental survey data