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
2. Major disease of wheat and barley
3. Source: Trail (2009) But also for other crops..
4. The rise of a species complex Phylogenetic species recognition based on genealogical concordance
5. FGSC species and trichothecene profile
6. 2012: Review on the complex
7. First review: FGSC species distribution No quantitative data on species frequency Authors' collection
8. First quantitative data from literature on FGSC distribution
9. Fusarium graminearum
10. Fusarium asiaticum
11. Thorough, but only narrative review - no quantitative data
12. First online database Limited to European continent
13. Maps and plots only in the article
14. Searchable and results in tabular format - no graphs and maps
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
16. Article info datatable
17. Strain info datatable
18. HTML report high quality plots Interactive dashboard: maps, plots & tables Data tables Computational work
19. RESULTS as of Feb 2020
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
21. Where are they published and impact? PNAS New Phytologist 35 mean = 2.71 median = 2.94
22. Number of articles per author 555 unique authors Authorship analysis: WordCloud Authors per article median = 7 (3 to 9)
23. Authorship analysis: Country of authors 33 countries
24. Authorship analysis: Country of authors 33 countries
25. Authorship collaboration networks Individual article no shared authorship Big nodes: several connections Center of large community Small isolated community
26. Country collaboration networks
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
28. Global coverage of sampling 105 articles 23,665 strains
29. FGSC species prevalence 23,665 strains
30. Strains by host – major crops
31. Strains by Chemotype – 3 major types
32. Correspondence analysis: host, specis and chemotype Small grains Maize Rice
33. Open Fusarium strain database Interactive dashboard: maps, graphs and tables https://emdelponte.github.io/FGSC/
34. Open Fusarium strain database Search any field Download results as XLS or PDF file
35. Ongoing and future > Submit the manuscript > Encourage authors to deposit raw data > Include links to FusariumID, Fusarium MLST, etc