The Rust Expression Browser – a new genomic tool for wheat rust researchers worldwide

The Rust Expression Browser – developed by John Innes Centre researchers – is the first gene expression browser to enable simultaneous interrogation of gene expression data for the notorious yellow rust pathogen and its wheat host.

This new web interface currently hosts 1,024 gene expression datasets in an easy ‘point-and-click’ format to improve access to these valuable but complex data resources. In particular, it hosts hundreds of datasets generated by use of the revolutionary, genomic based ‘field pathogenomics’ technique that was developed in the Saunders Lab.

The yellow rust fungus causes devastating losses to wheat production worldwide and is a serious constraint on UK wheat production.

In a new paper published in BMC Genomics, researchers describe the creation of this new tool and demonstrate its utility for accelerating wheat yellow rust research.

Flowchart illustrating the construction of the rust expression browser

RNA-Seq data was collated from 1024 Pst samples and pseduoaligned to the Pst reference transcriptomes and wheat transcriptome version 1.1 using kallisto, generating gene expression values (“Data preparation”). Metadata was gathered for each sample and loaded into a MySQL database. Data included where available (i) host species and variety, (ii) host developmental stage, (iii) host tissue type, (iv) fungicide treatment, (v) level of infection, and (vi) collection date and location information (“Metadata integration”). The publicly available expVIP code was cloned from GitHub and transferred to a virtual machine. Metadata, gene expression values and the reference transcriptome were then integrated into the rust expression browser, served to the internet using gunicorn (“Browser initiation”). 

Dr Thomas Adams, the first author said: “We are thrilled to be able to share the wealth of data collected over the years by the lab with the wider community. We hope this will make these datasets more accessible to all researchers, regardless of access to specialist computer systems or any experience with sequencing data.”

Dr Diane Saunders, the corresponding author, commented: “The Rust Expression Browser is a fantastic resource for the global community of rust researchers. This will undoubtedly lead to exciting new insight into the intricacies of the interaction between yellow rust and its wheat host.”

The development of this tool was made possible with the assistance of the John Innes Centre informatics team and the Computing infrastructure for Science team.

Source – John Innes Centre