Leveraging the heterogeneity between strains of Schizophyllum commune for functional genomics

Abstract

This thesis brings to light new S. commune strains that can be used to study interesting phenotypes like mushroom development at a high CO2 concentration, lignocellulose degradation and defense response. At the same time, it highlights how polymorphic this species is and how this complicates the genetic mapping of a trait of interest. In order to elucidate the functions of all genes in this mushroom-forming fungus, a combination of genetic tools is needed. Standard molecular profiling techniques like (comparative) genomics, (comparative) transcriptomics, proteomics, and metabolomics can help bring it one step further. Chromatin immunoprecipitation accompanied by deep sequencing or DNA affinity purification sequencing are techniques that can reveal direct interactions between transcription factors and their downstream genes. Although conventional BSA is an efficient method for functional analysis, there is great value in new BSA approaches like mutation mapping analysis pipelines for pooled RNA sequencing (Li et al., 2022; Li & Xu, 2022). Future advances in genotyping, phenotyping, and statistical approaches will most likely improve and develop new BSA tools.