Code repository for the discovery and cultivation of 'Ca. Chlorohelix allophototropha' strain L227-S17

Copyright Jackson M. Tsuji, Neufeld Research Group, 2024

This Github repository provides supplementary data files and code related to the publication by Tsuji and colleagues, 2024, "Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre," which is published in Nature. The pre-print version of the paper is also available on bioRxiv.

This repo also relies on a supplementary Zenodo data repository containing larger files, available here.

The main focus of this repo is the genomic analysis of "Candidatus Chlorohelix allophototropha", the first cultivated representative of a novel order (the "Ca. Chloroheliales") within the Chloroflexota phylum. "Ca. Chx. allophototropha" uses Type I photosynthetic reaction centers instead of Type II RC's like other phototrophs in the Chloroflexota phylum, and this has important implications for the evolution of photosynthesis. (Take a look at the paper linked above for more details.)

Repo contents

The following folders contain the content you might have come to this repo for:

• supporting_files - contains some key files used in the paper that aren't included in the supplementary data, like custom HMMs built for photosynthesis proteins associated with "Ca. Chx. allophototropha".
  • Some supporting files are too large for Github and are instead stored on Zenodo here
• analysis_code - shows code for analyses that we performed that weren't out-of-the-box. We also include miscellaneous code for data viz etc. performed in the paper, for those who are interested.

Analysis code: contents

The analysis_code folder is further divided into the following sub-folders:

• source_data - contains links to the different publicly available sequences datasets we used
• physiology - contains code and some small data files for analysis of spectroscopy data
• 16S_rRNA_gene_amplicon - shows the three different methods used to process 16S rRNA gene amplicon sequencing data in this work, and includes count table data.
• culture_metagenomics - includes code used to obtain genome bins from metagenomes of early enrichment cultures
• genomics - includes code for: hybrid assembly approaches used to obtain closed genome (bins), and read mapping to determine relative abundances across all genome bins from culture_metagenomics
• lake_omics - shows the analysis methods used to process lake metagenome/metatranscriptome data
• phylogenomics - code used to build the Chloroflexota species tree, search for photosynthesis genes among Chloroflexota members, and build phylogenies of photosynthesis-related genes

How to use this repo

Each of the major subfolders above contains a README file details about the folder contents and/or code. Some key usage cases for the repo include:

• Find supplementary files not included in the supplemental data in the paper
• Find how to download the datasets used in this paper
• Check how a certain analysis was performed
• Analyze a specific intermediate data file included in the repo

In general, it helpful to have the manuscript itself (see link at top of repo) on hand for comparison while reading this repo.

Versions of this repo

The Chlorohelix manuscript has been updated several times since the initial discovery of this exciting strain as we have added more experimental data. The following Github repo versions correspond to major versions of the manuscript:

• repo v4.0.0: corresponds to the published version of the manuscript in Nature, available here (2024)
• repo v3.0.0: corresponds to a second major manuscript revision here (2023)
• repo v2.0.1: corresponds to a major manuscript revision here (2021)
• repo v1.0.0: corresponds to the initial bioRxiv submission here (2020)

Citation

To cite this repo, please cite our main publication:

Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, Watanabe T, Fukui M, Hanada S, Tank M, Neufeld JD. Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature (2024). https://doi.org/10.1038/s41586-024-07180-y

Issues

To make this repo, I streamlined several aspects of the raw code to make it more presentable and easy to follow. As such, it is possible that syntax errors were introduced along the way. If you notice that any code block does not run, please post a Github issue, and I'll get back to you as soon as possible. You can also post an issue if you have questions/concerns about an aspect of the data analysis.

Enjoy!

Jackson M. Tsuji, PhD
On behalf of the manuscript's coauthor team