• Research

Understanding the invasion of the ash dieback pathogen

The ash dieback fungus may kill the majority of ash trees in the UK. We're trying to understand what the genome of this population invasion looks like so we can stop it.

Project summary.

Start date: February 2014

End date: February 2017

Duration: 3 years

Hymenoscyphus fraxineus (also known as Chalara) is a fungus that infects the leaves, stems and branches of the ash tree (Fraxinus excelsior). This fungal infection of ash trees is known as ash dieback and is visible first as blackened dead leaves and dark lesions at the base of dead side shoots. The disease will progress over subsequent years leading to dieback of branches in the crown of the tree and often death.

There are around 80 million mature ash trees in the UK. Ash makes up 5.5% of the nation’s total woodland cover or 13.3% of the broadleaved woodland. There are also an estimated 11–12 million “non-woodland” ash.  90–95% may die of the disease.

We are using a two-pronged approach which involves both assembling the genome of the tree in order to provide a resource for the scientific community to identify resistance and also to understand the genome of the pathogen and the genes that make it so devastating.


We have assembled the ash tree genome as well as the genome of the pathogen. We have also annotated the genes and re-sequenced 50 isolates (also sequenced at Edinburgh through collaboration with Mark Blaxter). This fungal genome assembly is very contiguous with most of the content assembled to just 23 scaffolds. Mapping individuals from within the EU and also from japan is allowing us to address questions on which genes harbour the greatest levels of polymorphism.

These data also allow us to assess the impact of a founder effect on a pathogen invasion and address the role of polymorphism (or lack of) and its importance in invasion success.



A hub for crowdsourcing information and genomic resources for Ash Dieback.


Technology used.

Genome sequencing of the pathogen was completed on the Illumina HiSeqs using two library types, a paired-end library and a longer mate pair library.


Our role in the genomics and population genomics of the ash dieback pathogen invasion fits within the Nornex consortium headed by Allan Downie (JIC).  This consortium encompasses a range of skills from across biology and focusses on a number of key areas:

  • Genomics of the pathogen Hymenoscyphus pseudoalbidus
  • Pathology of Hymenoscyphus pseudoalbidus
  • Chalara-resistant ash genome project
  • Mapping inheritance of low susceptibility in ash
  • Open access website

Impact statement.

Climate change, farming and human dispersal all make biological invasions more likely.  We must try to understand the processes involved in movement of pathogens and also the characteristics of those pathogens that successfully invade.  Here we a contributing to a large project (Nornex) where together we set out to identify resistance in the host tree and understand what makes the pathogen to virulent.