STARTING WITH TREE 35 – Ash genome reveals fungus resistance [16Jun13]

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

 

“POWER TO THE PEOPLE” – #Crowdsourcing genomic analyses of ash and ash dieback [12Feb13]

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

 

ASHES FROM ASHES – Making a one acre natural nursery [25Apr13]

This year, the winter’s work graduated from the young hazel coupes to the high forest. The objective was to fell 85 per cent of the trees, leaving only the very best oak trees, about 20 of the best ash and a few lucky birch trees to add a bit of variety. Of course, all the dastardly Holly had to be removed, too.

In two years, a crop of thousands of ash seedlings will sprout into the new light. Then all we have to do is keep the Holly regrowth in check and KEEP THE DEER OUT with a fence. The experts are saying that one in 10 trees are resistant. Lets say I have 10,000 seedlings … we would still have too many ash trees for the area. So let’s say, it is only one in a 1000 that are resistant, then we would still have 10 resistant trees, wouldn’t we? And that would be priceless.

http://worldwidewood.wordpress.com/2013/04/25/ashes-from-ashes-making-a-one-acre-natural-nursary/

 

NEED TO ENGAGE PRIVATE OWNERS – Assessing the impacts of ash dieback [16Mar13]

The majority of forest volume in the UK is not publicly owned – out of a total forest area of 3 million hectares in the UK, only 28% is managed by the Forestry Commission. For ash, this figure is much lower, with only 3% of ash woodlands not owned by the private sector.

For private owners, the costs of surveying, felling, and replacing ash trees are likely to be high, and the effects of this could be long-lasting. An increase in the amount of timber in the market could also drive prices down, affecting landowners even further.

For landowners to engage in monitoring ash dieback, resources must also be available for them to do so. The number of inquiries sent to the Forestry Commission’s Tree Health Diagnostic and Advisory Service has increased by 1000% over the past six months. As diseased trees come into leaf over spring, and more trees become infected when the Chalara fungus sporulates again in summer, this high workload could even increase.

The number of tree diseases present in the UK has risen exponentially over the past 20 years, and now, almost all tree species are under threat from at least one disease or pest. Red band needle blight and ash dieback threaten up to 18% of woodland in the UK.

The report compiled by Confor highlights that the extent of private ownership of ash woodlands needs to be taken in to account.

http://britishecologicalsociety.org/blog/blog/2013/03/15/assessing-the-impacts-of-ash-dieback/?utm_source=twitterfeed&utm_medium=twitter&utm_campaign=Feed%3A+EcologicalAndPolicyBlog+%28BES+Ecology+%26+Policy+Blog%29

 

ACCELERATED DISCOVERY – Is the high representation of fungal transcripts in the infected ash material unusual or alarming?

To accelerate discovery on Chalara ash dieback disease, sequence data from the ‘interaction transcriptome’ has been made available for ‘crowdsource’ analysis. Two different samples of infected material, AT1 and AT2, have been released thus far.

These examples demonstrate that the fraction of pathogen sequences in the interaction transcriptome may be large. Thus, we do not believe that it is particularly unusual or alarming that fungal sequences are estimated to account for 30% or more of the assembled transcripts in the AT1 sample.

http://oadb.tsl.ac.uk/?p=312

 

OPEN DATASETS – Crowdsourcing genomic analyses of ash and #ashdieback – power to the people [12Feb13]

Ash dieback is a devastating fungal disease of ash trees that has swept across Europe and recently reached the UK. This emergent pathogen has received little study in the past and its effect threatens to overwhelm the ash population. In response to this we have produced some initial genomics datasets and taken the unusual step of releasing them to the scientific community for analysis without first performing our own. In this manner we hope to ‘crowdsource’ analyses and bring the expertise of the community to bear on this problem as quickly as possible. Our data has been released through our website at oadb.tsl.ac.uk and a public GitHub repository.

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

 

ENIGMA CRACKING – Ash fungus genetic code unravelled [08Mar13]

UK scientists have unravelled the genetic code of the ash dieback fungus.

The DNA “blueprint” contains clues to how the pathogen attacks ash trees and possibly, in the long term, how to stop the epidemic, say genetic researchers.

A team at The Sainsbury Laboratory (TSL) and the John Innes Centre in Norwich sequenced the RNA of an infected ash twig in December.

They have now cracked the DNA sequence of three samples of the fungus in a matter of weeks.

The data is being published on the crowd sourcing website OpenAshDieBack in a £2.4m project funded by the Biotechnology and Biological Sciences Research Council.

A type of ash tree in Denmark, known as Tree 35, – which makes up 2% of the Danish ash tree population – has managed to survive the epidemic.

http://www.bbc.co.uk/news/science-environment-21433466

 

FIRST DATA – OpenAshDieBack: How useful is the AT1 assembly? [16Dec12]

There is a lesson from this first dataset. Whenever new or suspect plant diseases arise we should immediately sequence transcriptomes from field collected diseased tissue. These days the cost of an RNAseq lane is reasonable and the assemblies are pretty decent. The data generated should rapidly provide valuable information about the nature of the pathogen and offer an initial insight into its genes. Whenever time is of the essence, transcriptome sequencing should be initiated as soon as possible.

We decided early on in this project that speed would be a critical driver given the emergency nature of the problem. We decided that we should generate genetic sequences as rapidly as possible, release them to the community, and prompt the crowdsourcing exercise we have been publicizing since Friday.

http://oadb.tsl.ac.uk/?p=254

 

OPEN DATA NOW! – Scientists crowdsource to decode genetic code of ash dieback fungus [14Dec12]

Genetic data collected from infected trees in Ashwellthorpe wood in Norfolk will be posted on the Sainsbury Laboratory website this Friday at the new OpenAshDieback site, with the aim of finding out what makes the fungus that causes dieback attack the ash – and the best methods to halt or slow its spread.

Prof Sophien Kamoun, the head of the Sainsbury Laboratory, which is doing the work jointly with the John Innes Centre in Norfolk, said that scientific emergencies such as ash dieback made standard methods – where publication is peer-reviewed in secret and eventually published – too slow to be useful.

“I do have a beef with the way that research is typically done,” Kamoun said. “Scientists do genome sequencing but then hold onto it until it’s formally published. This isn’t appropriate in an emergency. Open sourcing the understanding of data in this way is totally adapted to the age of the internet.”

http://www.guardian.co.uk/environment/2012/dec/14/ash-dieback-scientists-crowdsourcing-fungus

 

NEW DATA SHARING INITIATIVE – OpenAshDieBack [15Dec12]

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

On this website you’ll be able to get data to do your own analyses on ash and ash dieback.
You can see the results of other peoples work as soon as it is available and share your own discoveries in the same way.

You will always get full credit for your work and in doing so contribute to a real community effort.

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