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Data from: Lichen fungi do not depend on the alga for ATP production

Citation

Tagirdzhanova, Gulnara (2021), Data from: Lichen fungi do not depend on the alga for ATP production, Dryad, Dataset, https://doi.org/10.5061/dryad.xgxd254gd

Abstract

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit of ATP synthase, from a few mitochondrial genomes. Here we show that while these fungi indeed have lost the mitochondrial ATP9, each retain a nuclear copy of this gene. Our analysis reaffirms that lichen fungi produce their own ATP.

Usage Notes

Here you can find data for the Tagirdzhanova et al. 2021 study (Lichen fungi do not depend on the alga for ATP production).

gc_cov_plots.zip is a compressed folder that contains the script, the README file, and the data to reproduce the GC/coverage plot used in the paper, as well as preliminary plots. To reproduce the analysis, decompress the folder and run the gc_cov_plots.R script. The folder contains:

  • data/GTX0158 contains the data files for producing GC/coverage plot for the Gomphillus americanus metagenome: metagenomic assembly (GTX0158_scaffolds.fasta), covergae file produced by CONCOCT (concoct_depth.txt), and binning file produced by CONCOCT (clustering_gt1000_merged.csv).
  • data/GTX0161 contains the data files for producing GC/coverage plot for the Alectoria fallacina metagenome: metagenomic assembly (GTX0161_scaffolds.fasta), coverage file produced by CONCOCT (concoct_depth.txt), and binning file produced by CONCOCT (clustering_gt1000_merged.csv).
  • data/GTX0163 contains the data files for producing GC/coverage plot for the Heterodermia speciosa metagenome: metagenomic assembly (GTX0163_scaffolds.fasta), coverage file produced by CONCOCT (concoct_depth.txt), and binning file produced by CONCOCT (clustering_gt1000_merged.csv).
  • data/TS1974 contains the data files for producing GC/coverage plot for the Imshaugia aleurites metagenome: metagenomic assembly (TS1974_scaffolds.fasta), coverage file produced by CONCOCT (concoct_depth.txt), and binning file produced by CONCOCT (clustering_gt1000_merged.csv).
  • gc_cov_plots.R is the script for producing the plots.
  • prelim_plots/ contains preliminary GC/coverage plots for each metagenomes used for finalizing the binning.
  • README.txt describes the analysis.

atp9_final_alignment.phylip is the alignment file used for reconstruction the ATP9 phylogeny.

atp9.contree is the file containing the ATP9 tree.

phylogenetic_analysis.md is a step-by-step description of how we made the phylogeny and dN/dS analysis.

metagenomics_analysis.zip contains scripts and details on the metagenomic analysis, including  

  • README.txt describing all the steps from the raw read data to genome annotations,
  • scripts/ folder contains all scripts used for this part of the analysis and referenced in README.txt,
  • output_MAG_annotations/ folder contains full GenBank files for each of the MAGs.

See also the github repo (https://github.com/metalichen/Lichen-fungi-do-not-depend-on-the-alga-for-ATP-production)