• Research

Understanding the genome, invasion and evolution of the Ash Dieback pathogen.

What does the genome of the ash dieback pathogen tell us about successful invaders?

Project summary.

Led by: Neil Hall and Mark McMullan

Funders:

UKRI Biotechnology and Biological Sciences Research Council (BBSRC)

Hymenoscyphus fraxineus 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, making it the UK’s third most common tree species. Ash makes up 5.5% of the nation’s total woodland cover (that’s 13.3% of broadleaved woodland) and there are also an estimated 11–12 million “non-woodland” ash.

Work by Richard Bugg and others (Kew Gardens) estimate that 60-100% of these trees will succumb to the disease. Moreover, we will hit a period of peak mortality in the coming years. 

Our work on the fungal invasion of Europe suggests that just two individuals were introduced to Europe (from East Asia) and they have gone on to devastate ash populations.

In preliminary analyses of native diversity from a single Japanese wood we showed that genetic diversity was eight times higher there than present across Europe. Genetic diversity is generally assumed to be a proxy for how adaptable a species is and so it is concerning that diversity is so high in a single wood. Given the devastation of the progeny of just two individuals we now want to understand the invasion process itself, could more individuals invade and, if so, what would be the impact of that introduction?

Details.

We are using a two-pronged approach to understand Ash Dieback:.

Understanding it’s evolution and population genomics:

A fungal invasion presents just a snapshot of the diversity present in the native range and this makes it difficult to understand a disease using this diversity alone. Further introductions of genetic diversity can be an important determinant for an increase in severity of invasions and this means it is important to understand the native diversity and the pathogen’s propensity to invade and evolve.

Our work on the population genomics of the ash dieback fungus shows us that the European population passed through an extreme bottleneck and quickly expanded into Europe. Analysis of genetic diversity present in Europe suggests that diversity present in the range from which invaders arrived was high. Preliminary estimates show that native genetic diversity is high and is present as non-synonymous diversity at putative effectors. However, this diversity is estimated based on a single wood in Japan whereas the native range also encoumpases large parts of China and Eastern Russia.

Furthermore, in Europe there is a signal of preservation of genetic diversity which indicates that structural genomic variation may operate to facilitate invasion. Fungi are known to employ numerous mechanisms which can preserve genetic variation through a bottleneck and also generate novel diversity. The implications of this structural genetic variation have generally been associated with rapid adaptation to new hosts. However, this variation may also be important in preserving and generating genetic variation through a bottleneck. It is important that we understand these processes in greater detail because as our climate changes and global trade increases we might have to deal with more fungal invasions.

Understanding its association with its Ash Host:

Despite the gloomy prognosis for European ash and the devastation that has already occurred, surveyance of Norfolk ash has provided reason for cautious optimism:

We have identified a large number of adult trees in areas known to contain ash dieback that appear to be significantly healthier than their neighbours. We intend to investigate exactly how these adult trees are surviving in such areas by comparing them with their diseased neighbours: are their natural defence mechanisms resisting infection or can they better tolerate it? In the native range, the fungus can complete its life cycle asymptomatically, i.e., without causing disease in its host – is something similar occurring here?

Furthermore, we have also identified populations of juveniles that seem to be thriving despite local susceptibility to ash dieback. Juvenile trees are usually more vulnerable to pathogens such as ash dieback than adults, so this has obvious implications for conservation because recovery of ash will require juveniles that can survive such an environment until reproductive age. Looking for differences in the genomes of these juveniles compared to local adults may elucidate any genetic component of juvenile survival.

Tools.

Genome Assembly

A combined MP and LMP version 2 assembly of the ash dieback pathogen genome (Hf-v2; see methods in https://www.nature.com/articles/s41559-018-0548-9)

https://opendata.earlham.ac.uk/opendata/data/Hymenoscyphus_fraxineus/EI/v2/assembly/

Genome data

All MP and LMP sequencing data generated for the Hf-v2.0 genome (PRJEB21027)

https://www.ebi.ac.uk/ena/data/view/PRJEB21027

Annotation data

The annotation built on that of the version 1 using data from the TSL OpenAshDieBack repository

http://oadb.tsl.ac.uk (see methods in https://www.nature.com/articles/s41559-018-0548-9).

https://opendata.earlham.ac.uk/opendata/data/Hymenoscyphus_fraxineus/EI/v2/annotation/

European single isolates 

Isolates were collected from across Europe and jointly sequenced at EI and at Edinburgh Genomics.  Isolates were also collected from Japan and sequenced at EI.  All but one of these were fruiting bodies which are a spore releasing stage and DNA is present from both the parental haplotypes but also their meiotic products.  One of these represents a single haploid isolate (PRJEB21027)

PRJEB21061

PRJEB21062

PRJEB21063

PRJEB21064

ERS480843–ERS480865

PRJEB21027

PRJEB21060

OpenAshDieBack

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

http://oadb.tsl.ac.uk/

Impact statement.

It is important that we understand the processes that lead to novel fungal invasions in greater detail because they may become more frequent as our climate changes and global trade increases. Considering the devastation already wrought on our native ash trees by such an invasion, it is also vital that we better comprehend the genetics underpinning juvenile survival of ash dieback - especially when acknowledging the potential for future invasions as ash dieback continues to evolve.

It is also a fascinating opportunity to highlight what makes a fungus pathogenic, by looking into the differences between Europe and Japan, where the ash dieback fungus does not cause disease.