General information

This repository contains the code and software environment definitions used to generate the datasets, results, tables and figures related to our modelling of tradeoff intensities in our paper 'Unraveling stress response trade-offs of drug resistance as actionable target in Nakasomyces (Candida) glabratus'.

Code

The code used can be found in the folder 'scripts', and 'Cglabrata_tradeoffs.yml' lists the software dependencies. Note that you can re-create the conda environment that we used with this command:

conda env create -n Cglabrata_tradeoffs_env -f Cglabrata_tradeoffs.yml

Data

The folder 'data' contains the following files related to mutations and annotations:

• 'SchikoraTamarit2024_Candida_glabrata_gene_features.tab' contains features of the gene annotations used here, as provided in our previous study (Schikora-Tamarit et. al. 2024, Nature Microbiology). It merges various annotations from the Candida Genome Database (CGD). Each row is one gene, and relevant fields are:

  • 'gff_upmost_parent': the gene ID.
  • 'gene_name': the gene name from CGD, if provided.
  • 'description': a description about gene function.
  • 'Scerevisiae_orthologs': the name of S. cerevisiae orthologs, if any.

• The files 'SchikoraTamarit2024_annotation_Candida_glabrata_<pathway_name>.tab' contain the mapping between gene IDs and GO, Reactome, Metacyc and Interproscan annotations, as provided in our study (Schikora-Tamarit et. al. 2024, Nature Microbiology).

• 'Ksiezopolska2021_all_new_variants_per_sample_WGS.tab' contains the variants appeared during drug adaptation in each evolved strain, as compared the WT parental. This file was generated by processing the supplementary tables of our previous study (Ksiezopolska et. al. 2021, Current Biology). Each row corresponds to one strain, and the fields are:

  • 'sampleID': the strain name.

  • 'final_name': the name of the feature affected, which may be a gene or a chromosome (in the case of aneuploidies). For genes, this integrates the information from SchikoraTamarit2024_Candida_glabrata_gene_features.tab fields 'gene_name', 'Scerevisiae_orthologs' and 'gff_upmost_parent'. It may be the 'gene_name', the 'Scerevisiae_orthologs' with a 'Scer_' suffix (if no 'gene_name' is defined) or the gene ID ('gff_upmost_parent', if none of the other fields are defined).

  • 'variant': the appeared variant. It can be missense mutation (e.g. mis|p.297|W/C), premature termination codon (e.g. PTC|p.611|W/*), frameshift (e.g. FS|p.233|E/X), in-frame deletion (e.g. del|p.657-658|YF/Y), in-frame insertion (e.g.ins|p.339|V/VE), loss of ATG (lostATG|c.1|Atg/Ttg), loss of stop codon (lostSTOP|c.1094|tAg/tCg), partial duplication (partial DUP), translocation (TRA), 5' deletion (5' DEL), deletion (DEL) or duplication (DUP).