Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression...

Area of Science:

• Plant pathology
• Genomics
• Bioinformatics

Background:

• Transcriptomics, particularly RNA-sequencing (RNA-Seq), offers insights into plant-pathogen interactions.
• The wheat yellow rust pathogen (Puccinia striiformis f. sp. tritici, Pst) presents unique challenges due to its obligate biotrophic nature.
• Novel RNA-Seq approaches like "field pathogenomics" enable studying Pst and wheat gene expression dynamics and population composition.

Purpose of the Study:

• To develop a comprehensive database and user-friendly browser for Pst and wheat gene expression data.
• To facilitate the analysis of large-scale transcriptomics datasets generated through field pathogenomics.
• To provide a valuable resource for researchers studying wheat rust pathosystems.

Main Methods:

• Generation of 538 new RNA-Seq datasets from Pst-infected field wheat samples.
• Analysis of these new datasets alongside 66 existing time-course datasets and 420 public field/lab samples.
• Development of the Rust Expression Browser (http://www.rust-expression.com) integrating gene expression values for Pst and wheat.

Main Results:

• Creation of a database with 1024 processed RNA-Seq datasets, doubling available transcriptomics data for this pathosystem.
• The Rust Expression Browser allows simultaneous "point-and-click" access to Pst and wheat gene expression profiles.
• Demonstrated utility by investigating Pst virulence gene expression and host plant responses.

Conclusions:

• The Rust Expression Browser provides significant value to the scientific community by enhancing data sharing and transparency.
• The database can be continuously expanded with new publicly available datasets.
• Facilitates deeper understanding of wheat rust pathogen biology and host interactions.