FGSCdb Tracking the global spread of species and chemotypes

FGSCdb is a database of information on characterized fungal strains of Fusarium graminearum species complex that encompasses a complex of species that cause head blight or scab of small grain crops, but also ear and stalk rot of maize and panicle blight in rice. Geographic location combined with the information on the year of sampling allows to track the temporal and spatial spread of the pathogen.

The data have been gathered directly from researchers or extracted from the published articles whenever the geographic information can be obtained. We would like to extend the utility of this project by allowing other researches to contribute data to populate the global map. Get in touch (delponte@ufv.br) to receive instructions on how to submit your data.

Transcript

1. FGSCdb
   Tracking the global spread
   of species and chemotypes
   EM Del Ponte, GM Moreira, CP Nicolli, TJ Ward,
   C Waalwijk, T van der Lee, Kerry O'Donnell, SN
   Chulze, SA Steinglein, D Pan, S Vero, Hao Zhang,
   DJ Tessmann, LJ Vaillancourt, A. Moretti, A.
   Logrieco
   Coordination Collaborators
   

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2. Major disease of wheat and barley
   

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3. Source: Trail (2009)
   But also for other crops..
   

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4. The rise of a species complex
   Phylogenetic species recognition based on genealogical concordance
   

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5. FGSC species and trichothecene profile
   

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6. 2012: Review on the complex
   

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7. First review: FGSC species distribution
   No quantitative data on species frequency
   Authors' collection
   

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8. First quantitative data from
   literature on FGSC distribution
   

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9. Fusarium graminearum
   

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10. Fusarium asiaticum
    

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11. Thorough, but only narrative
    review - no quantitative data
    

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12. First online database
    Limited to European continent
    

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13. Maps and plots
    only in the article
    

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14. Searchable and results in tabular
    format - no graphs and maps
    

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15. How to make it? … not alone. Need a great postdoc!
    Strain info
    Article info
    article_ID, pub_order, citation, DOI, title, author 1 to 14, journal_name,
    vol, num, pages, year, category_jcr, IF, n_citations, country_1 to 6,
    n_isolates, Fasi, Fboo, Fcor, Fgra, Fmer, Fnep, Fvor, Fasi_DON,
    Fasi_3ADON, Fasi_15ADON, Fasi_NIV, Fboo_DON, Fboo_15ADON,
    Fcor_15ADON, Fcor_NIV, Fgra_DON, Fgra_3ADON, Fgra_15ADON,
    Fgra_FUSX, Fgra_NIV, Fmer_DON, Fmer_15ADON, Fmer_NIV,
    Fnep_DON, Fvor_DON, Fvor_NIV, Fvor_4ANIV, country_1a to 3a,
    host_1 to 4.
    ID, Host,Organ, Cultivar, Location name, Country, Year, Latitude,
    Longitude, FGSC Species, ID method, Strain code, Collection code,
    Tri_genotype, Genotyping method, Chemotype, Chemotyping
    method,chemotyping substrate, Pub1, Pub2,Pub3,Comments
    Raw data from
    collaborators
    Screening and extracting
    data from articles' tables
    and supplementals
    -> FGSC species ID
    Dr. Glaucia Moreira
    

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16. Article info datatable
    

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17. Strain info datatable
    

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18. HTML report
    high quality plots
    Interactive dashboard: maps, plots & tables
    Data tables
    Computational work
    

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19. RESULTS
    as of Feb 2020
    

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20. Summary of article data: strain info and articles per year
    peer-reviewed articles
    2000 to 2020
    52 articles raw data on strain info
    33 strain info extracted from articles
    20 no strain info
    105
    

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21. Where are they published and impact?
    PNAS
    New Phytologist
    35 mean = 2.71
    median = 2.94
    

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22. Number of articles per author
    555 unique authors
    Authorship analysis: WordCloud
    Authors per article
    median = 7 (3 to 9)
    

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23. Authorship analysis: Country of authors
    33
    countries
    

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24. Authorship analysis: Country of authors
    33
    countries
    

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25. Authorship collaboration networks
    Individual article
    no shared authorship
    Big nodes: several connections
    Center of large community
    Small isolated community
    

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26. Country collaboration networks
    

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27. Strain summary info - as of Feb. 2020
    105
    articles
    8,843 11,062
    3,760
    23,665
    14,822
    not geotagged
    raw data from authors
    With known location
    available in the paper
    Reported location
    Included in the strain
    DB and map
    

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28. Global coverage of sampling
    105 articles
    23,665
    strains
    

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29. FGSC species prevalence
    23,665
    strains
    

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30. Strains by host – major crops
    

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31. Strains by Chemotype – 3 major types
    

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32. Correspondence analysis: host, specis and chemotype
    Small grains
    Maize
    Rice
    

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33. Open Fusarium strain database
    Interactive dashboard: maps, graphs and tables
    https://emdelponte.github.io/FGSC/
    

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34. Open Fusarium strain database
    Search any field
    Download results as
    XLS or PDF file
    

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35. Ongoing and future
    > Submit the manuscript
    > Encourage authors to deposit raw data
    > Include links to FusariumID, Fusarium MLST, etc
    

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