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Conrad Schoch    Keith Seifert    John Spouge    Vincent Robert    Elena Bolchacova    Pedro Crous,    &…1
and a cast of thousands…    (…or more than 140 collaborators from 20 countries)2
Aime MC An K-D Bai F-Y Barreto R Begerow D Bergeron M-J Blackwell    M Boekhout T Bogale M Bolchacova E Boonyuen N Burgaz ...
Keeling et al. 2005    Fungi within Eukaryotes                 ‘true’ Fungi4
Ascomycota                       Basidiomycota                          Glomeromycota    FUNGI                          ‘e...
Subphylum:Saccharomycotina   Ascomycotan vs Chordate diversity                                                            ...
The Fate of Cox1 for Fungal Barcoding  – Fungal Cox1 gene is full of introns     • up to eleven introns     • intron mobil...
Fungal DNA barcoding workshop             Amsterdam April 20118
http://www.fungalbarcoding.org    Vincent Robert    Biolomics & CBS9
10
Pezizomycotina               Ascomycota     Saccharomycotina     Genes:    Dikarya        Taphrinomycotina     ITS        ...
Ascomycota     Elena Bolchacova     LifeTech           Basidiomycota12
Pezizomycotina                                Saccharomycotina                                Taphrinomycotina            ...
Coverage : Samples in Species     Pezizomycotina                     Basidiomycota                                        ...
The Status of a Species’s                 Nearest Neighbor List     For each species in the dataset, the nearest neighbor ...
Individual PCIs         Pezizomycotina   Basidiomycota Saccharomycotina Early diverging   AllS=SSUR=RPB1L=LSUI=ITS        ...
Combined 4 gene comparison        (746 strains, 396 spp)      SSU      RPB1      LSU      ITS17
Combined 6 gene comparison       (207 strains, 55 species)       SSU       RPB2       RPB1       MCM7       LSU       ITS18
Barcode Gap Analysis     SSU                RPB1     LSU                 ITS19
Pairwise comparisons ITS           (2972 strains)20
PCR Success21
ITS (Internal Transcribed Spacer) Sequencing                         (ms. in review at PNAS)     Advantages       Universa...
What comes next? Secondary markers• Penicillium   – ITS, -tubulin• Trichoderma   – ITS, TEF1• Fusarium   – TEF1, RPB1, RPB...
JGI Community Sequencing Program1000 fungal genomes over5 yearsWhere does barcoding fit?
What else is out there?                         Cryptomycota       Jones et al. 2011. Nature 474: 200-203.        Rosling ...
Environmental diversity – real or virtual species?        Hibbett et al. 2011. Fungal Biology Reviews 25: 38-47.
We need to become more efficient (and better) at             describing fungal diversityTwo commonly found Fungi – no sequ...
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Conrad Schoch - Saturday Closing Plenary

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Conrad Schoch - Saturday Closing Plenary

  1. 1. Conrad Schoch Keith Seifert John Spouge Vincent Robert Elena Bolchacova Pedro Crous, &…1
  2. 2. and a cast of thousands… (…or more than 140 collaborators from 20 countries)2
  3. 3. Aime MC An K-D Bai F-Y Barreto R Begerow D Bergeron M-J Blackwell M Boekhout T Bogale M Bolchacova E Boonyuen N Burgaz AR Buyck B Cai L Cardinali G Chaverri P Chen W Crespo A , Crous PW Damm U de Hoog S DeBeer ZW Del-Prado R Diéguez-Uribeondo J Divakar PK Douglas B Dueñas M Duong TA Duong V Eberhardt U Elshahed MS Fliegerova K García MA Ge Z-W Griffith GW Griffiths K Groenewald JZ Groenewald M Gryzenhout M Guo L-D Hagen F Hambleton S Hamelin RC Hansen K Ho H-M Hofstetter V Högnabba F Hong S-B, Hosaka K Houbraken J Hughes K Huhndorf S Huhtinen S Hyde KD James T Johnston PR , Jones EBG Kirk P Kõljalg U Kovacs GM Kurtzman CP Landvik S Leavitt SD Levesque A Liggenstoffer AS Liimatainen K Lombard L Luangsa-ard JJ Lumbsch HT Maganti H Martin MP May T Meyer W Miller AN Mongkolsamrit S Nagy L Nilsson RH Niskanen T Nyilasi I Okada G Okane I Olariaga I Otte J Papp T Park D Petkovits T Pino-Bodas R Qing C Quaedvlieg W Raja HA Redecker D Rintoul T Robert V Ruibal C Ruibal C Sarmiento-Ramírez JM Schindel D Schmitt I Schoch CL Seifert KA Shearer C Sotome K Spouge J Stefani FOP Stenroos S Stockinger H Suetrong S , Suh S-O Surname Initials, Suzuki M Tanaka K Tedersoo L , Telleria MT Tretter E Untereiner WA Urbina H Vágvölgyi C Vialle A Voigt K Vu D Walther G Weir BS Weiß M Xu JP, Yahr R Yang Z-L Yurkov A Zamora JC Zhang N Zhuang W-Y3
  4. 4. Keeling et al. 2005 Fungi within Eukaryotes ‘true’ Fungi4
  5. 5. Ascomycota Basidiomycota Glomeromycota FUNGI ‘early diverging’ lineages zygomycetes, chytrids, Microsporidia Oomycetes Green plants5 From James et al., Nature 2006 0.2
  6. 6. Subphylum:Saccharomycotina Ascomycotan vs Chordate diversity Phylum:Chordata The Scientist6
  7. 7. The Fate of Cox1 for Fungal Barcoding – Fungal Cox1 gene is full of introns • up to eleven introns • intron mobility – These introns • interfere with primer design • often prevent successful PCR amplification Zasmidium nocoxi – Multiple paralogs were unexpected Crous – Complete gene varies from 1584–22006 bp in fungi Barcode
  8. 8. Fungal DNA barcoding workshop Amsterdam April 20118
  9. 9. http://www.fungalbarcoding.org Vincent Robert Biolomics & CBS9
  10. 10. 10
  11. 11. Pezizomycotina Ascomycota Saccharomycotina Genes: Dikarya Taphrinomycotina ITS Ustilaginomycotina Agaricomycotina LSU Basidiomycota Pucciniomycotina SSU Glomeromycota RPB1 Mortierellomycotina Mucoromycotina RPB2 Kickxellomycotina MCM7 Zoopagomycotina Fungi Entomophthoromycotina Chytridiomycota Neocallimastigomycota Blastocladiomycota Microsporidia rozellid clade Nucleariida11 Mesomycetozoa
  12. 12. Ascomycota Elena Bolchacova LifeTech Basidiomycota12
  13. 13. Pezizomycotina Saccharomycotina Taphrinomycotina Ustilaginomycotina John Spouge Agaricomycotina NCBI Pucciniomycotina Glomeromycota 746 strains, 396 species Mortierellomycotina Mucoromycotina Divided into 4 sets Kickxellomycotina 4 markers each Zoopagomycotina Entomophthoromycotina Chytridiomycota Neocallimastigomycota Blastocladiomycota Microsporidia rozellid clade Nucleariida13 Mesomycetozoa
  14. 14. Coverage : Samples in Species Pezizomycotina Basidiomycota 49 genera 84+142=226 species 49+43=92 species 83 416 samples 202 140 samples Saccharomycotina B ‘Early diverging’ lineages 36+13=49 species 21+8=29 species 85 samples 43 samples14
  15. 15. The Status of a Species’s Nearest Neighbor List For each species in the dataset, the nearest neighbor list is either Correct for every sample Correct for some but not all samples Correct for no samples Percent correct identification (PCI) In the dataset, calculate the fraction of species where the nearest neighbor list is correct for every sample1515
  16. 16. Individual PCIs Pezizomycotina Basidiomycota Saccharomycotina Early diverging AllS=SSUR=RPB1L=LSUI=ITS The fraction of species where the nearest neighbor list is correct for every sample16
  17. 17. Combined 4 gene comparison (746 strains, 396 spp) SSU RPB1 LSU ITS17
  18. 18. Combined 6 gene comparison (207 strains, 55 species) SSU RPB2 RPB1 MCM7 LSU ITS18
  19. 19. Barcode Gap Analysis SSU RPB1 LSU ITS19
  20. 20. Pairwise comparisons ITS (2972 strains)20
  21. 21. PCR Success21
  22. 22. ITS (Internal Transcribed Spacer) Sequencing (ms. in review at PNAS) Advantages Universal primers Large available dataset Strong demand from espcially ecologists Problems Shortage of data in many groups Differences in multiple copies Often lack of resolution at species level Can be difficult to align above genus or family22
  23. 23. What comes next? Secondary markers• Penicillium – ITS, -tubulin• Trichoderma – ITS, TEF1• Fusarium – TEF1, RPB1, RPB2 Trichoderma spirale
  24. 24. JGI Community Sequencing Program1000 fungal genomes over5 yearsWhere does barcoding fit?
  25. 25. What else is out there? Cryptomycota Jones et al. 2011. Nature 474: 200-203. Rosling et al. 2011. Science 333: 876-879.
  26. 26. Environmental diversity – real or virtual species? Hibbett et al. 2011. Fungal Biology Reviews 25: 38-47.
  27. 27. We need to become more efficient (and better) at describing fungal diversityTwo commonly found Fungi – no sequence data, no culturesBactridium flavum Sphaerosporium lignitile

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