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Fusarium graminearum species complex: Global database and mapping species and chemotypes

Fusarium graminearum species complex: Global database and mapping species and chemotypes

Fusarium graminearum is ranked among the ten most dangerous fungal pathogens that affect agro-ecosystems. It causes floral diseases in small grains including wheat, barley and oats, as well as summer crops such as maize and rice. Infected kernels are light-weight and may be contaminated with mycotoxins of concern to human and animal health, mainly trichothecenes and zearalenone. The increased availability of F. graminearum strains collected worldwide, from different hosts/substrates, together with advances in taxonomy based on genealogical concordance, led to the recognition of species, as part of the Fusarium graminearum species complex (FGSC), during the 2000s. Surveys of FGSC strains have been conducted and reported worldwide for different crops/substrates, with strains being accurately identified to species, including novel species within the complex, using DNA barcoding methods. In addition, the potential to produce mycotoxins, mainly B-trichothecenes, is determined using either chemical methods or, more commonly, time and cost-effective PCR-based assays that target portions of genes of the trichothecene biosynthetic (TRI) cluster. We conducted a systematic review of peer-reviewed studies reporting lineages/species within FGSC. Two main data tables were created. The first, contained data at the article level including bibliographic, scientometric, geographic, methodological (ID methods), host surveyed and FGSC species. A second data table contained information at the strain level such as article, code(s), host/substrate, year, geographical coordinates, species and trichothecene genotype. In this talk, bibliographic and scientometric analyses of the data obtained from 77 peer-reviewed articles authored by 323 authors and published in 27 journals that matched the criteria (as of August 2018) will be presented. A summary of the data at the strain level for a total of 14,553 catalogued strains will be presented as part of a website, the global FGSC database. The interactive dashboard (accessible at: https://github.com/emdelponte/FGSC) allows for searches, summarization and mapping of strains according to several criteria including article, country, host, species and trichothecene genotype. The FGSC database may be useful for guiding future surveys and exploring factors associated with species distribution such as climate and land use. This work is supported by CNPq and Mycokey project.

Emerson M. Del Ponte

September 17, 2018
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  1. Fusarium graminearum species complex:
    Global database and mapping species and chemotypes
    Emerson M. Del Ponte, Gláucia M. Moreira,
    Carolina B. Pereira, Dauri J. Tessmann, Todd J. Ward, Kerry
    O'Donnell, Cees Waalwijk, Theo van der Lee, Zhang Hao,
    Sofia N. Chulze, Sebastian A. Steinglen, Dinorah Pan,
    Silvana Vero, Antonio Moretti and Antonio Logrieco
    16 to 18 Sep 2018 - Wuhan China
    2nd Mycokey International Conference
    Integrated Solutions for Mycotoxin Management

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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. Primarily, a yield-limiting disease...
    Attainable yield 4,000 kg
    20% FHB index
    Actual yield:
    3,000 to 3,200 kg
    Duffeck et al (unpublished)
    Paul et al. (2010)

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  5. … but produces mycotoxins
    Del Ponte et al (2012)
    Duffeck et al. (2017)
    Deoxynivalenol and nivalenol (Brazilian wheat)
    Zearalenone (Brazilian wheat)

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

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  7. FGSC species and trichothecene profile

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  8. 2012: Review on the complex

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

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  10. First quantitative data from
    literature on FGSC distribution

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  11. Fusarium graminearum

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  12. Fusarium asiaticum

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

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  14. First online database
    Limited to European continent

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  15. Maps and plots
    only in the article

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

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  17. From a Lab electronic collection to a global database!
    How about a
    Pan-American
    database? I have
    US and CAN data.
    We should go Global!!
    Let's invite Zhang Hao
    and Moretti.
    I accept! I will send
    you all Chinese
    data I have in two
    days!!
    Of course! I Will send
    you the data in... two
    months, ok?
    February 2017 - Tropical Fusarium workshop in Brazil
    I presented an electronic collection FGSC strains from my Lab.

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  18. 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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  19. Article info datatable

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  20. Strain info datatable

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  21. HTML report
    high quality plots
    Interactive dashboard: maps, plots & tables
    Data tables
    My job: script dev.

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  22. Summary of article data: strain info and articles per year
    peer-reviewed articles
    2000 to 2018
    40 articles raw data on strain info
    23 strain info extracted from articles
    14 no strain info
    77

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  23. Where are they published and impact?
    27
    PNAS

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  24. Number of articles per author
    323 unique authors
    Authorship analysis: WordCloud

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  25. 27
    countries
    Authorship analysis: Country of authors

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

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  27. 14,553 strains
    Strain summary info - as of Sep. 2018

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  28. Strain information: genotype by species
    14,553 strains

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  29. Correspondence analysis

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  30. Open Fusarium strain database
    Interactive dashboard: maps, graphs and tables

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

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  32. Future work
    > Submit a manuscript to Toxins
    > Get the new website up and running!
    > Encourage authors to deposit raw data
    > Include links to FusariumID, Fusarium MLST, etc
    > Extend to other species complex

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  33. Universidade Federal de Viçosa
    謝謝

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