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.

Transcript

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
2. Major disease of wheat and barley
3. Source: Trail (2009) But also for other crops..
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)
5. … but produces mycotoxins Del Ponte et al (2012) Duffeck et al. (2017) Deoxynivalenol and nivalenol (Brazilian wheat) Zearalenone (Brazilian wheat)
6. The rise of a species complex Phylogenetic species recognition based on genealogical concordance
7. FGSC species and trichothecene profile
8. 2012: Review on the complex
9. First review: FGSC species distribution No quantitative data on species frequency Authors' collection
10. First quantitative data from literature on FGSC distribution
11. Fusarium graminearum
12. Fusarium asiaticum
13. Thorough, but only narrative review - no quantitative data
14. First online database Limited to European continent
15. Maps and plots only in the article
16. Searchable and results in tabular format - no graphs and maps
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.
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
19. Article info datatable
20. Strain info datatable
21. HTML report high quality plots Interactive dashboard: maps, plots & tables Data tables My job: script dev.
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
23. Where are they published and impact? 27 PNAS
24. Number of articles per author 323 unique authors Authorship analysis: WordCloud
25. 27 countries Authorship analysis: Country of authors
26. Authorship collaboration networks Individual article no shared authorship Big node: several connections Center of large community Small isolated community
27. 14,553 strains Strain summary info - as of Sep. 2018
28. Strain information: genotype by species 14,553 strains
29. Correspondence analysis
30. Open Fusarium strain database Interactive dashboard: maps, graphs and tables
31. Open Fusarium strain database Search any field Download results as XLS or PDF file
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
33. Universidade Federal de Viçosa 謝謝