Abstract
We have established the Ustilago bromivora-Brachypodium spp. interaction as a new model pathosystem for biotrophic fungal plant infections of the head smut type (Rabe et al., 2016). In this protocol, the methodology used for comparing gene expression between saprophytic and in planta growth of the fungus is described. The experimental and analytical pipeline, how next generation RNA sequencing (Illumina RNA-Seq) analysis can be used to obtain lists of genes significantly up or down regulated in planta in comparison to axenic culture is given. Furthermore, different methods to identify functional categories that are over- or under-represented among specific classes of genes are presented.
Highlights
[Background] RNA deep sequencing (RNA-Seq) is a powerful and versatile tool to gain insights into the responses of cells and organisms to environmental changes and their adaptations to new developmental stages
A striking change of life situation comes with the switch from yeast-like growth to filamentous, pathogenicity associated growth modes in non-obligate pathogens. We studied this switch in the biotrophic fungal plant pathogen Ustilago bromivora (Rabe et al, 2016)
Over/underrepresentation analysis (ORA) is a method to link expression changes to potential biological responses by looking if certain classes of transcripts respond in a concerted way
Summary
[Background] RNA deep sequencing (RNA-Seq) is a powerful and versatile tool to gain insights into the responses of cells and organisms to environmental changes and their adaptations to new developmental stages. The experimental and analytical pipeline, how generation RNA sequencing (Illumina RNA-Seq) analysis can be used to obtain lists of genes significantly up or down regulated in planta in comparison to axenic culture is given.
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