Scripts, pipelines, and analysis details for the Tagirdzhanova et al. 2021 study (avaliable as a preprint)
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.
- Metagenomics analysis describes all the steps from the raw read data to genome annotations and contains the pipelines we used.
- GC_cov plots contains the script and data to produce the GC/coverage plot used in the paper, as well as other preliminary graphs.
- Pylogenetic analysis contains the details on how we made the phylogeny and dN/dS analysis and contains the tree file and the alignment.