DOI: 10.5061/dryad.xgxd254gd
title: Data from: Lichen fungi do not depend on the alga for ATP production

description: 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.
description: Here you can find data for the Tagirdzhanova et al. 2021 study
 (Lichen fungi do not depend on the alga for ATP production).
 <strong>gc_cov_plots.zip</strong> 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: 
 <strong>data/GTX0158</strong> 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). 
 <strong>data/GTX0161 </strong>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). 
 <strong>data/GTX0163 </strong>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). 
 <strong>data/TS1974 </strong>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). 
 <strong>gc_cov_plots.R</strong> is the script for producing
 the plots. <strong>prelim_plots/
 </strong>contains preliminary GC/coverage plots for each metagenomes
 used for finalizing the binning. 
 <strong>README.txt</strong> describes the analysis.
 
 <strong>atp9_final_alignment.phylip</strong> is the
 alignment file used for reconstruction the ATP9 phylogeny.
 <strong>atp9.contree</strong> is the file containing
 the ATP9 tree.
 <strong>phylogenetic_analysis.md</strong> is a
 step-by-step description of how we made the phylogeny and dN/dS
 analysis.
 <strong>metagenomics_analysis.zip</strong> contains
 scripts and details on the metagenomic analysis, including  
 <strong>README.txt
 </strong>describing all the steps from the raw read data to genome
 annotations, 
 <strong>scripts/</strong> folder contains all scripts used for
 this part of the analysis and referenced in README.txt,
 <strong>output_MAG_annotations/ </strong>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)