Yellow Rust Nextstrain Browser

Visualise the spread and development of yellow rust strains through online publicly accessible data.

The following guide provides an introduction to viewing the Nextstrain database for first time users

Nextstrain is an open-source project aiming to harness the potential of pathogen genome data through real-time updated surveys coupled with analytic and visualisation tools. This project currently hosts analyses of eleven human pathogens: from the ebola and influenza viruses through to the infectious bacterium tuberculosis. Our use of this platform for analysis of wheat yellow rust (Puccinia striiformis f. sp. tritici) therefore represents the first plant pathogenic fungus to be analysed with this system. The analysis is available at

Through an interactive web-based interface a user can directly interact with the analysis results to focus on results of most interest to them. For instance, by default the isolates are coloured by genetic group, this can be toggled to show the country of origin of the isolate, as shown below.


By default, the map panel shows the location of isolates by country, the greater the radius of the circle, the more isolates it represents. This can be toggled to show more specific location information, again with the radius of the circle being proportional to the number of isolates it represents.


In order to visualise a region of the tree in more detail, a specific branch can be zoomed to. This is done simply by selecting the branch representing all the individuals of interest, as shown below.


A large amount of metadata for each sample is available from the phylogeny panel. These can be easily viewed through selecting a node, which creates a pop-up box containing all the available metadata for this sample.


Finally, the nextstrain system allows the download of several key files, including: the tree in newick format, metadata by strain and by author and finally an image of the default tree in svg format. This link is located at the bottom of the page.


This guide was created by Thomas Adams of Diane Saunders’ lab at the John Innes Centre