Conrad Schoch Keith Seifert John Spouge Vincent Robert Elena Bolchacova Pedro Crous , &…

1. An Official Barcode for Fungi Conrad Schoch Keith Seifert John Spouge Vincent Robert Elena Bolchacova Pedro Crous, &…

2. and a cast of thousands… (…or more than 140 collaborators from 20 countries)

3. Aime MC An K-D Bai F-Y BarretoR Begerow D Bergeron M-J Blackwell M Boekhout T BogaleM Bolchacova E Boonyuen N BurgazAR BuyckB Cai L CardinaliG Chaverri P Chen W Crespo A , Crous PW Damm U de Hoog S DeBeer ZW Del-Prado R Diéguez-UribeondoJ Divakar PK Douglas B DueñasM Duong TA Duong V Eberhardt U ElshahedMS Fliegerova K GarcíaMA 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 HögnabbaF Hong S-B, Hosaka K Houbraken J Hughes K Huhndorf S HuhtinenS Hyde KD James T Johnston PR , Jones EBG Kirk P Kõljalg U Kovacs GM Kurtzman CP Landvik S Leavitt SD Levesque A Liggenstoffer AS LiimatainenK Lombard L Luangsa-ard JJ Lumbsch HT MagantiH Martin MP May T Meyer W Miller AN MongkolsamritS Nagy L Nilsson RH NiskanenT NyilasiI Okada G OkaneI OlariagaI OtteJ Papp T Park D Petkovits T Pino-BodasR Qing C Quaedvlieg W Raja HA Redecker D Rintoul T Robert V Ruibal C Ruibal C Sarmiento-RamírezJM Schindel D Schmitt I Schoch CL Seifert KA Shearer C SotomeK Spouge J Stefani FOP Stenroos S Stockinger H Suetrong S , Suh S-O Surname Initials, Suzuki M Tanaka K Tedersoo L , TelleriaMT Tretter E Untereiner WA Urbina H VágvölgyiC Vialle A Voigt K Vu D Walther G Weir BS Weiß M Xu JP, Yahr R Yang Z-L YurkovA Zamora JC Zhang N Zhuang W-Y

4. ‘true’ Fungi Keeling et al.2005 Fungi within Eukaryotes

5. Ascomycota Basidiomycota Glomeromycota FUNGI ‘early diverging’ lineages zygomycetes, chytrids, Microsporidia Oomycetes Green plants From James et al., Nature 2006 0.2

6. Ascomycotanvs Chordate diversity Subphylum:Saccharomycotina Phylum:Chordata The Scientist

7. Barcode 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 • Multiple paralogs were unexpected • Complete gene varies from 1584–22006 bp in fungi ZasmidiumnocoxiCrous

8. Fungal DNA barcoding workshop Amsterdam April 2011

9. http://www.fungalbarcoding.org Vincent Robert Biolomics & CBS

11. Pezizomycotina Ascomycota Saccharomycotina Genes: ITS LSU SSU RPB1 RPB2 MCM7 Taphrinomycotina Dikarya Ustilaginomycotina Agaricomycotina Basidiomycota Pucciniomycotina Glomeromycota Mortierellomycotina Mucoromycotina Kickxellomycotina Zoopagomycotina Fungi Entomophthoromycotina Chytridiomycota Neocallimastigomycota Blastocladiomycota Microsporidia rozellid clade Nucleariida Mesomycetozoa

12. Ascomycota Elena Bolchacova LifeTech Basidiomycota

13. Pezizomycotina Saccharomycotina Taphrinomycotina Ustilaginomycotina Agaricomycotina John Spouge NCBI Pucciniomycotina Glomeromycota 746 strains, 396 species Divided into 4 sets 4 markers each Mortierellomycotina Mucoromycotina Kickxellomycotina Zoopagomycotina Entomophthoromycotina Chytridiomycota Neocallimastigomycota Blastocladiomycota Microsporidia rozellid clade Nucleariida Mesomycetozoa

14. Coverage : Samples in Species Pezizomycotina Basidiomycota 84+142=226 species 416 samples 49 genera 83 species 140 samples 49 genera 83 species 140 samples 49+43=92 species 202 samples Saccharomycotina B ‘Early diverging’ lineages 36+13=49 species 85 samples 21+8=29 species 43 samples

15. The Status of a Species’sNearest 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 sample 15

16. Individual PCIs Pezizomycotina Basidiomycota Saccharomycotina Early diverging All S=SSU R=RPB1 L=LSU I=ITS The fraction of species where the nearest neighbor list is correct for every sample

17. Combined 4 gene comparison (746 strains, 396 spp) SSU RPB1 LSU ITS

18. Combined 6 gene comparison (207 strains, 55 species) SSU RPB2 RPB1 MCM7 LSU ITS

19. Barcode Gap Analysis RPB1 SSU LSU ITS

20. Pairwise comparisons ITS (2972 strains)

21. PCR Success

22. ITS (Internal Transcribed Spacer) Sequencing (ms. in review at PNAS) Advantages • Universal primers • Large available dataset • Strong demand from espciallyecologists 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 family

23. What comes next? Secondary markers Penicillium ITS, -tubulin Trichoderma ITS, TEF1 Fusarium TEF1, RPB1, RPB2 Trichodermaspirale

24. JGI Community Sequencing Program 1000 fungal genomes over 5 years Where does barcoding fit?

25. What else is out there? Cryptomycota Jones et al. 2011. Nature 474: 200-203. Roslinget al. 2011. Science 333: 876-879.

26. Environmental diversity – real or virtual species? Hibbett et al. 2011. Fungal Biology Reviews 25: 38-47.

27. We need to become more efficient (and better) at describing fungal diversity Two commonly found Fungi – no sequence data, no cultures BactridiumflavumSphaerosporiumlignitile