The genetic insights could eventually be used to cross Tree 35 with breeding stock from our native ash population. Tree 35 is predominantly female and the genetic make-up could help identify a predominantly male UK tree with resistance to make a breeding pair. Or it could be used to identify both female and male UK trees with similarly low susceptibility to the fungus. A combination of crosses might be needed for a lasting comeback from the epidemic.

Ash trees are almost always fertilised by pollen from another ash tree rather than by self-pollination. This generates two copies of each chromosome in the resulting seeds. Although very similar, the chromosomes tend to have many differences when you look at the detail. This ‘heterozygosity’ makes it difficult to generate a genome sequence because in effect you have to put two genomes together at the same time.

Tree 35 has been identified as highly heterozygous.

http://www.tgac.ac.uk/home/news/54/68/Genome-sequence-for-mother-of-ash-dieback-survival/

The scientists are extremely hopeful that, having determined the tree’s complete set of genetic material – through a process known as genome sequencing – they have paved the way to identify those genes which might be connected to its ability to withstand the fungus.

Although the breakthroughs have raised hopes that a new breed of ash will be able to grow and survive in the face of the fungus, they will do nothing to protect Britain’s 80m existing ash trees, which are all under threat.

Adult clones of tree 35 grown from cuttings taken from the original trees in the 1930s were recently discovered on the Danish island of Sealand. [However] just planting this variety of Ash in the UK would result in a narrow genetic base making the species vulnerable to future diseases, experts said, adding that the latest breakthroughs still represented a giant step forward for the long-term prospects of the tree in this country.

http://www.independent.co.uk/news/uk/home-news/genetic-secrets-of-resistant-tree-gives-new-hope-over-ash-dieback-disease-8660992.html

Scientists have sequenced the genome of a type of ash tree with resistance to the deadly fungal disease sweeping the UK.

The development could be the starting point for breeding a strain of ash to replace thousands expected to succumb to ash die-back in the next few years.

All the data is being put on a crowd sourcing website OpenAshDieBack to enable experts from around the world to help identify genes that might be connected to the trees’ ability to withstand the fungus.

These genes could then be part of a breeding programme for resistant trees.

The samples for the latest research came from so-called “tree 35”, a strain of ash from Denmark originally bred nearly 100 years ago, which has shown an ability to tolerate the fungal disease, when virtually all its Danish relatives were wiped out.

Prof Allan Downie of the John Innes Centre believes this genetic understanding of both the lethal fungal infection and the surviving strain could help fill the impending gap in the canopy.

“We’re trying to give nature a bit of a helping hand by identifying the right kind of (native) trees to do the appropriate crosses,” he said.

http://www.bbc.co.uk/news/science-environment-22913111

The Genome Analysis Centre (TGAC) has worked fast to sequence and assemble the valuable genome of the survivor “tree 35” from the recent Ash Dieback outbreak that have caused devastating damage to the Danish Ash woodlands and that now threatens the UK trees.

This information will be useful to those that are trying to find the trees that would offer at least a partial resistance and can be used to replace the now empty woodlands and remediate the damage.

This work contributes to the Nornex consortium, part of the Biotechnology and Biological Sciences Research Council (BBSRC) and Defra funded bioscience response to ash dieback (Chalara fraxinea). Prof. Erik Dahl Kjær and his group have been instrumental in the success of this project, read more about his work on this here.

“The genome sequence of this ash will be an essential tool that can help us to follow the inheritance of the ability of some ash trees to tolerate and to inhibit the growth of the Chalara fraxinea pathogen. Such knowledge will help generate new varieties of ash trees that can withstand attack by the fungus,” said Prof. Allan Downie at the John Innes Centre.

http://www.tgac.ac.uk/news/52/68/Unravelling-the-genetic-code-of-the-Ash-Dieback-survivor-tree-35/

Genetic resistance to ash dieback disease is to be studied at a Suffolk Wildlife Trust (SWT) nature reserve.

Scientists from the Forestry Commission are using the site at Arger Fen and Spouse’s Grove, near Sudbury, to study genetic resistance to the Chalara fungus – which causes the disease.

About 15 different strains of ash will be planted on the five acre site later this week.

The trust responded to a request from the Forestry Commission for sites.

http://www.bbc.co.uk/news/uk-england-suffolk-22484952

To kick start genomic analyses of the pathogen and host, we took the unconventional step of rapidly generating and releasing genomic sequence data. We released the data through our new ash and ash dieback website, oadb.tsl.ac.uk, which we launched in December 2012. Speed is essential in responses to rapidly appearing and threatening diseases and with this initiative we aim to make it possible for experts from around the world to access the data and analyse it immediately, speeding up the process of discovery. We hope that by providing data as soon as possible we will stimulate crowdsourcing and open community engagement to tackle this devastating pathogen.

We have generated and released Illumina sequence data of both the transcriptome and genome of Chalara and the transcriptome of infected and uninfected ash trees. We took the unusual first step of directly sequencing the “interaction transcriptome” [2] of a lesion dissected from an infected ash twig collected in the field. This enabled us to respond quickly, generating useful information without time-consuming standard laboratory culturing; the shortest route from the wood to the sequencer to the compute

Most importantly, crowdsourcing allows for a new form of potentially effective live peer-review, many sets of eyes interrogating and reviewing data and analyses mean that unusual results are quickly highlighted and can be assessed and dealt with appropriately. Whether they are eventually found to be inconsistencies in analysis or more exciting genuine new discoveries, the end product is brought to the scientific community many times faster than the usual peer-review by a small number of reviewers and crucially it all happens out in the open with maximum transparency. The cornerstone of our crowdsourcing is our repository on GitHub [4], a versioning system designed for collaboration in software development that automatically maintains attribution of contribution, meaning that whoever contributes will get full credit for the difference that they made. We are certain that the data will prove useful to anyone who wishes to be involved in the fightback against ash dieback and that concerted, early data-sharing and open analysis is a crucial step in a productive and timely response to emergent pathogen threats.

Our initiative is an early step towards developing the crucial function of the digital immune system for response to plant pathogens; the thing we cannot upload to a repository is the people with the expertise and the will to contribute, and that is why we need the scientific community to download our data and provide analyses.

http://www.gigasciencejournal.com/content/2/1/2

The main objective of the project was to heighten biosecurity efforts against by developing a method based on a portable deoxyribonucleic acid (DNA) testing machine that can diagnose ash dieback within 30 minutes.
The project was supported under the EU’s ‘Food, agriculture and fisheries, and biotechnology’ (KBBE) programme to the tune of EUR 3 million.

Read more at: http://phys.org/news/2013-04-ash-dieback-fungus.html#jCp

This is the first genome assembly release of the British Ash Tree Genome project. It is based on 4.3X coverage of the ash genome by Roche 454 sequencing, and assembled using Newbler and the CLC Genome Finishing Module by Lizzy Sollars. The options used in Newbler to make this assembly were: ‘-sl 32’, ‘-urt’, ‘-m’, ‘-e 5’. Ten other assemblies with different options were carried out in Newbler, and this assembly was selected on the basis of higherst contig N50 length and highest number of complete hits of core eukaryote genes using CEGMA (a search for 248 ultra-conserved core eukaryote genes). Statistics for this assembly are as follows:

http://ashgenome.org/data

Should we start planting Ash with natural Chalara resistance even if they aren’t of UK provenance, e.g. Danish ‘Tree 35′?

AD: We should be very clear that tree 35 is not ‘resistant’. It tolerates the fungus better than most but it still gets infected. We do not know what is likely to happen with such trees over 20-40 years. The plan it to see if there are different genetic determinants in different trees that tolerate the fungus. If there are, it may be possible to cross them with each other and combine the characters to increase tolerance.

DM: It isn’t certain whether ‘Tree 35′ is going to be tolerant against the UK population of ash dieback. Tree 35 has shown to have great tolerance, but it isn’t clear how it will be in 20 – 30 years and we want to be able to create long term resistance. That said, there are great lessons to be learned from the genetic makeup of this tree and understanding how it has reached this tolerance is going to be of great benefit. In the end we would like to achieve a UK population of resistant trees, with UK-specific diversity, as our tree population is genetically different from the Danish population.

JW: Before we can go ahead with widespread planting of ash trees such as Tree 35, we have to be sure about the extent of its resistance.  However, just because trees/seeds are not of UK provenance doesn’t mean we should exclude them.  The releases from a number of programmes breeding for resistance to Dutch elm disease have made use of a wide range of elm species from Asia to produce resistant elms.  Also, many of the broadleaf trees planted in Britain, including oaks raised after the Napoleonic wars, have depended on seed from other European countries.

http://oadb.tsl.ac.uk/?p=371

The fast-track research funding has been awarded to gather an in-depth understanding of the ash dieback fungus and to provide genetic clues about some ash trees’ natural resistance to attack. Computer models will also be built to develop monitoring plans for the distribution and spread of the fungus, as well as charting how the disease might progress. This knowledge will help to fight the fungus and replace lost trees with those more able to survive.

Professor Sarah Gurr from Biosciences is leading the University of Exeter group in the Nornex consortium that has been awarded the funding. The group includes Prof Murray Grant, Dr Chris Thornton, Dr David Studholme, Professor Gero Steinberg and Professor Nick Talbot. The consortium brings together tree health and forestry specialists with scientists working with state-of-the-art genetic sequencing, biological data and imaging technologies to investigate the molecular and cellular basis of interactions between the fungus and ash trees.

Led by Professor Allan Downie at the John Innes Centre (JIC), the consortium includes: the University of Exeter, The Sainsbury Laboratory, East Malling Research, The Genepool at the University of Edinburgh, The Genome Analysis Centre, the Food and Environment Research Agency, Forest Research, the University of Copenhagen and the Norwegian Forest and Landscape Institute. The research will also complement a project funded by the Natural Environment Research Council (NERC) at Queen Mary University of London to decipher the ash tree’s genetic code.

BBSRC Chief Executive Professor Douglas Kell said: “This agile funding response will ensure we improve our understanding of this devastating tree disease as quickly as possible. Little is known about the fungus, why it is so aggressive, or its interactions with the trees that it attacks. This prevents effective control strategies