Ash tree genome aids fight against disease

Tens of millions of ash trees across Europe are dying from the Hymenoscyphus fraxinea fungus - the most visible signs that a tree is infected with ash dieback fungus are cankers on the bark and dying leaves.

Project leader Dr Richard Buggs from QMUL's School of Biological and Chemical Sciences said: "This ash tree genome sequence lays the foundations for accelerated breeding of ash trees with resistance to ash dieback."

A small percentage of ash trees in Denmark show some resistance to the fungus and the reference genome is the first step towards identifying the genes that confer this resistance.

The ash tree genome also contains some surprises. Up to quarter of its genes are unique to ash. Known as orphan genes, they were not found in ten other plants whose genomes have been sequenced.

Dr Buggs added: "Orphan genes present a fascinating evolutionary conundrum as we have no idea how they evolved."

This research is published today in the journal Nature. It involved a collaboration between scientists at: QMUL, the Earlham Institute, Royal Botanic Gardens Kew, University of York, University of Exeter, University of Warwick, Earth Trust, University of Oxford, Forest Research, Teagasc, John Innes Centre, and National Institute of Agricultural Botany.

The reference genome from QMUL was used by scientists at York University who discovered genes that are associated with greater resistance to ash dieback. They have used these to predict the occurrence of more resistant trees in parts of the UK not yet affected by the disease, which is spreading rapidly.

The genome sequence will also help efforts to combat the beetle Emerald Ash Borer, which has killed hundreds of millions of ash trees in North America.

Ash trees have a huge significance in culture and society - they are one of the most common trees in Britain and over 1,000 species, from wildflowers to butterflies, rely on its ecosystem for shelter or sustenance. Ash timber has been used for years for making tools and sport handles, for example hammers and hockey sticks, and is used often for furniture.

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The work was funded by NERC, BBSRC, Defra, ESRC, the Forestry Commission, the Scottish Government, Marie Sklodowska-Curie Actions, Teagasc - the Agriculture and Food Development Authority.

Notes to editors

'Genome sequence and genetic diversity of European ash trees' by E. Sollars et al is published in the journal Nature on Monday 26 December 2016.

DOI 10.1038/nature20786.

QMUL press office contact: Neha Okhandiar (n.okhandiar@qmul.ac.uk / 07834 039266)

For further details, images or to arrange interviews with the author please contact the press office.

Appendix 1

Supportive press release from University of York:

Could disease 'tolerance' genes give new life to UK ash trees?

Researchers at the University of York have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection, which has the potential to wipe out 90% of the European ash tree population.

The disease, called ash dieback, was first identified in Poland, where it devastated the native ash tree population. It rapidly spread across northern Europe, and was discovered in the UK in 2012.

Results from the latest study, a collaboration between the University of York and Queen Mary University of London, could contribute to breeding new varieties of ash that are tolerant to the disease.

The disease is aggressive, spreads quickly through the population, and has no cure, other than individual natural tolerance to the infection. It is spread on the wind or via the transfer of infected saplings between areas. Symptoms include loss of leaves and lesions, which are a useful way to diagnose fungal ash dieback, as they leave a characteristic diamond shape scar on the bark.

Professor Ian Bancroft, plant biologist at the University of York, said: "This disease has spread across Europe in less than 10 years so there is some urgency to understand how we can better support breeding programmes for the species.

"Ash trees can be found in home gardens, parks, and roadsides and are an important woodland species that support a number of insects and fungi. It is not known exactly how the loss of this tree species will impact the eco-system, but from past examples, we know that the extinction of any species can fundamentally alter the environment."

The York team had previously tested a genetic screening process on Danish trees. Using this data alongside information from the ash tree genome, which was sequenced by researchers at Queen Mary University of London (QMUL), they were able to improve the genetic markers for disease tolerance, and use them to predict the tolerance of a sample of trees from across the UK.

Early indications suggest that the proportion of UK trees with tolerance to ash dieback is greater than that of the Danish and Polish trees, but it is still unknown whether the UK trees have previously been infected with the disease and built tolerance or whether their genetic tolerance is yet to be tested.

Dr Andrea Harper, plant biologist at the University of York, said: "Working with DEFRA, the next stage of this work will be to establish a UK panel suitable for identifying additional, UK-specific, markers for tolerance. This will improve our predictions on individual trees, and provide more information about why some trees are tolerant to the disease. It will also support breeding programmes to develop tolerant varieties of ash."

The research, funded by BBSRC and Defra, is published in the journal, Nature.

For further information:

University of York
Press Office, Samantha Martin,
+44 (0)1904 322029

Appendix 2:

Supportive press release from University of Exeter and University of Warwick:

Ash dieback: Insect threat to fungus-resistant trees

Ash trees which can resist the killer dieback fungus may be more vulnerable to attacks by insects, according to new research.

Scientists from the universities of Exeter and Warwick examined trees which are resistant to ash dieback and - unexpectedly - found they had very low levels of chemicals which defend against insects.

With efforts under way to protect ash trees from dieback, the scientists warn that selecting trees for fungal resistance could put them at risk from insects.

Aside from ash dieback, the other major threat to European ash trees is the Emerald Ash Borer beetle, which has already devastated vast tracts of ash in the USA and is currently spreading westwards across Europe.

"Our research highlights the danger of selecting trees for resilience to ash dieback at the expense of resistance to insects that threaten this iconic UK tree species," said joint lead author Dr Christine Sambles, of the University of Exeter.

"Ash dieback, which is caused by a fungus called Hymenoscyphus fraxineus, can kill young trees in a season, while older trees tend to decline and die over several years."

The research, published in the journal Nature, is part of a study involving several universities and Government institutes which looked at the DNA of ash trees in the hope of identifying ash dieback resistance.

Instead of focussing on DNA, the Exeter and Warwick scientists looked at differences in chemical composition between tolerant and susceptible ash trees.

"Plants use a vast range of chemicals to defend against fungal attack, and the primary objective was to identify differences which could be used to screen young ash trees and choose the best ones for replanting," said co-author Professor Murray Grant, Elizabeth Creak Chair in Food Security at the University of Warwick.

"Our findings underline the need for further research to ensure that we select ash trees resilient to present and future threats."

Co-author Dr David Studholme, of the University of Exeter, added: "These findings highlight Exeter's world-class expertise in high-impact, integrative plant science underpinned by key research infrastructure, such as the Mass Spectrometry facility."

For further information:

University of Exeter
Press Office
+44 (0)1392 724828
pressoffice@exeter.ac.uk

Appendix 3

Supportive release from National Institutes of Bioscience

Disease tolerant genes renew hope for UK ash trees

Researchers have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection that has the potential to wipe out 90% of the European ash tree population.

The disease, called ash dieback, was first identified in Poland, where it devastated the native ash tree population. It rapidly spread across northern Europe, and was discovered in the UK in 2012.

Results from the latest study published in Nature, a UK collaboration between Queen Mary University of London (QMUL), University of York, Earlham Institute (EI), John Innes Centre (JIC), NIAB and the University of Copenhagen, could contribute to breeding new varieties of ash that are tolerant to the disease.

Much like Dutch elm disease, ash dieback is aggressive, spreads quickly through the ash tree population, and has no cure, other than individual natural tolerance to the infection. It is spread on the wind or via the transfer of infected saplings between areas. Symptoms include loss of leaves and lesions, which are a useful way to diagnose fungal ash dieback, as they leave a characteristic diamond-shaped scar on the bark.

The York team had previously tested a genetic screening process on Danish trees identified by collaborators at the University of Copenhagen as having a range of different levels of disease susceptibility. Using this data alongside information from the ash tree genome, which was sequenced by researchers at QMUL by utilising EI's reference gene models, they were able to improve the genetic markers for disease tolerance, and use them to predict the tolerance of a sample of trees from across the UK.

Leading to these research findings, EI (previously 'The Genome Analysis Centre') generated the transcriptome and re-sequencing (together with the Institute's previous analysis of the resistant 'Tree 35' from Denmark released in 2013) data to conduct the bioinformatics analysis of the UK ash tree, in alignment with the Nornex Consortium to combat Ash Dieback, funded by DEFRA and BBSRC. The analysis was carried out on a subset of the tree's genetic regions, with high coverage across the samples. This increased the number of potential markers that could be used to sustain ash tree diversity for breeding programmes.

EI also sequenced 37 trees originating from across Europe to investigate genomic diversity in ash. The data were analysed by researchers at QMU, JIC and NIAB finding evidence for apparent long-term decline in effective population size. The EI team generated the most comprehensive annotation of ash genes to date, and this will aid researchers in identifying genetic variants linked to specific traits associated with the killer tree disease. This will help seek out the suspected tolerant genes and support future breeding programmes of ash trees with low susceptibility to the disease.

Dr David Swarbreck, Regulatory Genomics Group Leader at EI, said: "Having a more comprehensive annotation of ash genes has improved the identification of markers for ash dieback and will aid future functional studies into this prevalent disease."

Professor Mario Caccamo, previously at EI, now Head of Crop Bioinformatics at NIAB, added: "This effort is a great example of team-work across several leading UK research organisations responding to the devastating threat of ash dieback. The identification of markers for tolerance will be a very important tool in the toolbox that complements other ongoing efforts to manage the threat of this disease. We have also generated important genomic resources that will support other studies and offer the foundations for more research into tackling the epidemic."

Professor Allan Downie, Emeritus Fellow at JIC and coordinator of the NORNEX programme, commented: "This work represents significant new progress in our understanding of ash dieback disease and the patterns of inheritance of tolerance to this disease. Our success has been built on excellent national and international collaborations. These have brought the strengths of genomics and transcriptomics research in the UK together with the excellent analyses of disease susceptibility done in Denmark, to enhance our research into UK ash trees. This progress has been breath-taking in its speed and as a research coordinator based at JIC; I have been delighted by the spirit of collaboration and determination brought to this project by my Danish and UK collaborators.

Early indications suggest that the proportion of UK trees with tolerance to ash dieback is greater than that of the Danish and Polish trees, but it is still unknown whether the UK trees have previously been infected with the disease and built tolerance or whether this is due to their genetic tolerance, is yet to be tested.

The study, "Genome sequence and genetic diversity of European ash trees" is published in the journal, Nature.

Appendix 4:

Supportive release from Royal Botanic Gardens, Kew

Ash tree genome sequence is breakthrough for addressing disease

A team of scientists have successfully decoded the genetic sequence of the ash tree, to help the fight against the fungal disease, ash dieback.

In a paper published by the journal Nature today, a team of researchers led by Richard Buggs, who heads up plant health research at the Royal Botanic Gardens, Kew, assembled a reference genome and analysed the diversity of ash trees throughout Europe. Their collaborators have used this resource to identify genes that may be associated with low susceptibility to ash dieback. They used these to predict the effect that ash dieback will have on ash trees all over Britain.

The genome sequence will also help efforts to combat the beetle Emerald Ash Borer, which has already killed hundreds of millions of ash trees in North America.

Project Leader Dr Richard Buggs, Senior Research Leader (Plant Health) at RBG Kew who conducted the work at Queen Mary University of London's (QMUL) School of Biological and Chemical Sciences said: "This is the first time a plant genome has been rapidly sequenced in response to an emerging disease threat, leading to an assessment of the susceptibility of as yet uninfected populations. Kew is continuing to work with the latest genomic technologies to increase the armoury of methods that can be deployed against plant pests and pathogens."

There are 520 specimens of the Ash tree at Kew and its Sussex site, Wakehurst (227 of these are at Kew). At Kew's Millennium Seed bank scientists are also involved in gathering seed of different ash populations around Britain to help inform broader efforts to control disease spread and drive plant health policy.

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