May 2013


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/

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The images were obtained using cryo scanning electron microscopy, where the sample is plunged into liquid nitrogen to freeze it and imaged using the electron microscope.

The benefit of this method is that the sample is imaged in as close to its natural state as possible, providing the best quality 3D view of an organism.

http://news.jic.ac.uk/2013/05/close-up-images-of-chalara-fraxinea/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+NewsFromTheJohnInnesCentre+%28News+from+the+John+Innes+Centre%29

 

The South East has been declared a “low priority” area – authorities say that because the disease is already widespread, it is not cost effective to tackle it.

Dr Alun Griffiths, microbiologist and chairman of the Kent Men of the Trees conservation charity, said the county needed better protection.

“I’ve been studying diseases around the world all my professional life,” he said.

“I’ve always thought that if you have a focus, an area where disease is being spread rapidly, that would be the place where you’d put most of your effort.

The government is planting thousands of young ash trees in the region as part of a research trial, including at the Hucking Estate near Maidstone.

Scientists hope 1% of them may survive and develop resistance in a decade’s time.

http://www.bbc.co.uk/news/uk-england-kent-22510873

 

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

Ash dieback has been found in mature trees for the first time in Wales.

The infected trees were discovered in Ferryside, Carmarthenshire, by Natural Resources Wales (NRW) staff last week.

Until now the Chalara dieback in Wales had been confined to newly planted sites in trees from nurseries known to hold infected stock.

http://www.bbc.co.uk/news/uk-wales-22516757

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

I am particularly excited that the Real Life Science Studio in the John Hope Gateway will be hosting the Virtual Landscape Theatre for one week from 8th August. This interactive exhibit allows an audience to decide what actions should be taken to reduce the impact of ash dieback and to explore the implications of these choices. Intrigued? Come and find out more in August!

Diseases are a real threat to our trees and it is likely we will loose a high proportion of our ash trees. Yet, over the course of this project I started to feel more positive about the future of Scottish woodlands. It would be easy to listen to the mass media and get very depressed about the state of our forests and trees. But woodlands are dynamic and have always changed; over such long periods of time we humans find it difficult to comprehend.

We need to build resilience in the woodlands of Scotland to ensure their longevity. By this I mean managing woodlands in a way that creates diversity in the species present, diversity in the age of the trees and diversity in structure. If we do this it may be possible to maintain the ever-changing, unique woodlands of Scotland.

http://stories.rbge.org.uk/archives/2051