• NCG

Responding to emergencies with genomics

What happens when you get an outbreak of a disease? You sequence it to tell you where it’s come from, how it’s spreading and most importantly how to combat it.

Project summary.

Start March 2012

Duration Ongoing

One of the pillars of the BBSRC National Capability in Genomics at EI is the use of our technologies to respond to emergencies where required. Our tools are largely high-throughput sequencing machines and this means we can do genomic characterisation, not just of emerging pathogens, but also their host species.

We’re proud to have played a part in the Nornex consortium efforts to characterise Ash dieback disease. Members of the Platforms and Pipelines Group delivered RNA-Seq and DNA sequencing data of the pathogen, but also generated the data underlying the differences between resistant and susceptible trees.

However pathogens don’t stop evolving, and consequently we remain ready to characterise the next threat to emerge. Currently we work closely with the field pathogenomics approaches developed by Dr Diane Saunders keeping track of emerging rust pathogens of wheat.

Details.

One of the primary reasons to generate sequence data is to look for genetic variation. When we’re dealing with an outbreak, sequencing a number of isolates from different locations as a pathogen spreads allows you to infer relationships between them, also called phylogenies, which trace its evolution. This variation may explain why a pathogen is able to spread - has it been able to transfer to a new host? Has it been able to overcome the defences of a host that normally resists infection quite well? Is the pathogen being transferred through human or environmental activity?

Genetic variation can also tell us about resistance to disease, we don’t always have to look at the pathogen, we can look at the host to help us pinpoint where resistance is occurring by comparing different responses to infection by an organism.

For the Nornex consortium work, we generated several data sets, genomic DNA and RNA-Seq data on Illumina platforms, but have continued to deliver long-read sequencing on the PacBio to improve annotations of the Ash tree genomes we’re working on. Our work supporting field pathogenomics approaches has been mostly RNA-Seq and genomic sequencing of the the pathogens on Illumina platforms, but we always look at how the other technologies in our lab can help people generate and release data faster on emerging threats.

Data.

Open Wheat Blast

http://www.wheatblast.net
In February 2016, wheat blast was spotted in Bangladesh– its first report in Asia. Wheat is the second major food source in Bangladesh, after rice. The blast disease has, so far, caused up to 90% yield losses in more than 15000 hectares. Scientists fear that the pathogen could spread further to other wheat growing areas in South Asia.

Wheat Yellow Rust

http://yellowrust.com/
One of wheats worst enemies is wheat yellow rust, a disease responsible for yield losses of up to 70 percent or complete crop loss if the disease occurs early in the growing season.

Nornex

http://nornex.org/
Nornex is a network of scientists from eleven research institutions aiming to make tools to help understand how to deal with ash dieback, caused by Chalara fraxinea (Hymenoscyphus pseudoalbidus)

Collaborators.

Nornex

http://nornex.org/

Nornex is a network of scientists from eleven research institutions aiming to make tools to help understand how to deal with ash dieback, caused by Chalara fraxinea (Hymenoscyphus pseudoalbidus)

Impact statement.

Allowing researchers to interrogate pathogen outbreaks rapidly is an essential tool in being able to combat their spread. Whether a bacterial or viral outbreak in humans, or a fungal outbreak on an important crop, understanding the evolution of pathogens, and mechanisms of resistance to diseases can be a turning point in mitigating against their future spread.