Adaptation of Ustilago maydis SG200 to hydrogen peroxide (H₂O₂)

Repository created by Jorge Cuamatzi-Flores

Repository with scripts to reproduce the analysis and figures presented in: Enhanced Oxidative Stress Resistance in Ustilago maydis and Its Implications on the Virulence

Bioinformatic analysis of sequenced genomes

In this experiment we sequenced by short-reads the genome of U. maydis SG200 and UmH₂O₂-R

Pipeline to process the fastq files:

The raw fastq of the sequenced genomes of U. maydis SG200 and the adapted H₂O₂ strain are accessible on NCBI with accession numbers SRR25650020 and SRR25650011, respectively.

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

SNP Calling

See the 03_SNP_Calling subdirectory

Analysis of collected data

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)

Manuscript Figures

See the subdirectory 04_USMA_Data_Growth_qPCR_Infection

Supplementary Material

See the 05_SupplementaryMaterial subdirectory