Format

Send to

Choose Destination
Bio Protoc. 2017 Aug 5;7(15). pii: e2426. doi: 10.21769/BioProtoc.2426.

Overrepresentation Analyses of Differentially Expressed Genes in the Smut Fungus Ustilago bromivora during Saprophytic and in planta Growth.

Author information

1
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
2
Vienna Biocenter Core Facilities (VBCF), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.

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.

KEYWORDS:

Biotrophic plant pathogens; Differential expression; Fungal pathogens; Plant infection; RNA-seq; Smuts; Ustilago bromivora; over/under representation analysis

Supplemental Content

Full text links

Icon for PubMed Central
Loading ...
Support Center