Experimental evolution of Ustilago maydis SG200 under oxidative stress

Repository created by Jorge Cuamatzi-Flores

Repository with scripts to reproduce the analysis and figures presented in: [insert link to paper here]

Bioinformatic analysis of sequenced genomes in the experimental evolution

Pipeline to process the fastq files:

All raw fastq files used for this research are available at NCBI (BioProject Id: PRJNA1005765).

The document Data_Sheet_to_Download_Fastq_Files.csv in the main directory ~/Umaydis_experimental_Evolution contains the accession number assigned to each sample.

Cleaning

See the 01_Cleaning subdirectory

Mapping and coverage plotting

See the 02_MappingAndCoveragePlotting subdirectory

The Figure 3 of the main manuscript can be found in 02_MappingAndCoveragePlotting/Figures/Plot_USMA_521_v2_9.Log2Ratio.png

SNP Calling

See the 03_SNP_Calling subdirectory

Analysis of sequenced pools

See the 04_Pools_analysis subdirectory

The Figure 4 of the main manuscript can be found in 04_Pools_analysis/Figure_Variants.Pools.png

Analysis of chromosomal duplications in U. maydis isolates

See the 05_Duplications_in_Umaydis_isolates subdirectory

Analysis of data collected from experimental evolution, analysis of gene expression of UMAG_11067 and phenotypic analysis of oexUMAG_11067 (strain that overexpress UMAG_11067 gene)

See the subdirectory 06_USMA_ExpEvol_Data

The Figures 1, 2, 5, 6, and 7 of the main manuscript can be found in 06_USMA_ExpEvol_Data/Figures/