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Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community

Diane Saunders, Kentaro Yoshida, Christine Sambles, Rachel Glover, Bernardo Clavijo, Manuel Corpas, Daniel Bunting, Suomeng Dong, Ghanasyam Rallapalli, Matthew D. Clark, David Swarbreck, Sarah Ayling, Matthew Bashton, Steve Collin, Tsuyoshi Hosoya, Anne Edwards, Lisa Crossman, Graham Etherington, Joe Win, Liliana Cano, David J. Studholme, J. Allan Downie, Mario Caccamo, Sophien Kamoun, View ORCID ProfileDan MacLean
doi: https://doi.org/10.1101/004564
Diane Saunders
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Kentaro Yoshida
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Christine Sambles
2The University of Exeter, Department of Biosciences, Stocker Road, Exeter, EX4 4QD, UK
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Rachel Glover
3The Food and Environment Research Agency, Sand Hutton, York, UK, YO41 1LZ
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Bernardo Clavijo
4The Genome Analysis Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Manuel Corpas
4The Genome Analysis Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Daniel Bunting
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Suomeng Dong
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Ghanasyam Rallapalli
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Matthew D. Clark
4The Genome Analysis Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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David Swarbreck
4The Genome Analysis Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Sarah Ayling
4The Genome Analysis Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Matthew Bashton
5Newcastle University, Newcastle upon Tyne, UK, NE1 7RU
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Steve Collin
6Norfolk Wildlife Trust, Foxley Wood, Norfolk, UK, NR20 4QR
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Tsuyoshi Hosoya
7National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan
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Anne Edwards
8The John Innes Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Lisa Crossman
9SequenceAnalysis.co.uk, Norwich Research Park, Norwich, UK, NR4 7UH
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Graham Etherington
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Joe Win
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Liliana Cano
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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David J. Studholme
2The University of Exeter, Department of Biosciences, Stocker Road, Exeter, EX4 4QD, UK
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J. Allan Downie
8The John Innes Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Mario Caccamo
4The Genome Analysis Centre, Norwich Research Park, Norwich, UK, NR4 7UH
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Sophien Kamoun
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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Dan MacLean
1The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, NR4 7UH
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  • ORCID record for Dan MacLean
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Abstract

Ash dieback is a fungal disease of ash trees caused by Hymenoscyphus pseudoalbidus that has swept across Europe in the last two decades and is a significant threat to the ash population. This emergent pathogen has been relatively poorly studied and little is known about its genetic make-up. In response to the arrival of this dangerous pathogen in the UK we took the unusual step of providing an open access database and initial sequence datasets to the scientific community for analysis prior to performing an analysis of our own. Our goal was to crowdsource genomic and other analyses and create a community analysing this pathogen. In this report on the evolution of the community and data and analysis obtained in the first year of this activity, we describe the nature and the volume of the contributions and reveal some preliminary insights into the genome and biology of H. pseudoalbidus that emerged. In particular our nascent community generated a first-pass genome assembly containing abundant collapsed AT-rich repeats indicating a typically complex genome structure. Our open science and crowdsourcing effort has brought a wealth of new knowledge about this emergent pathogen within a short time-frame. Our community endeavour highlights the positive impact that open, collaborative approaches can have on fast, responsive modern science.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 25, 2014.
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Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community
Diane Saunders, Kentaro Yoshida, Christine Sambles, Rachel Glover, Bernardo Clavijo, Manuel Corpas, Daniel Bunting, Suomeng Dong, Ghanasyam Rallapalli, Matthew D. Clark, David Swarbreck, Sarah Ayling, Matthew Bashton, Steve Collin, Tsuyoshi Hosoya, Anne Edwards, Lisa Crossman, Graham Etherington, Joe Win, Liliana Cano, David J. Studholme, J. Allan Downie, Mario Caccamo, Sophien Kamoun, Dan MacLean
bioRxiv 004564; doi: https://doi.org/10.1101/004564
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Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community
Diane Saunders, Kentaro Yoshida, Christine Sambles, Rachel Glover, Bernardo Clavijo, Manuel Corpas, Daniel Bunting, Suomeng Dong, Ghanasyam Rallapalli, Matthew D. Clark, David Swarbreck, Sarah Ayling, Matthew Bashton, Steve Collin, Tsuyoshi Hosoya, Anne Edwards, Lisa Crossman, Graham Etherington, Joe Win, Liliana Cano, David J. Studholme, J. Allan Downie, Mario Caccamo, Sophien Kamoun, Dan MacLean
bioRxiv 004564; doi: https://doi.org/10.1101/004564

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