1. Conrad Schoch
Keith Seifert
John Spouge
Vincent Robert
Elena Bolchacova
Pedro Crous,
&…
1

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

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-Y
3

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

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

6. Subphylum:Saccharomycotina Ascomycotan vs Chordate diversity
Phylum:Chordata
The Scientist
6

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. Fungal DNA barcoding workshop
Amsterdam April 2011
8

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

10. 10

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
Nucleariida
11
Mesomycetozoa

12. Ascomycota
Elena Bolchacova
LifeTech Basidiomycota
12

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
Nucleariida
13
Mesomycetozoa

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 samples
14

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 sample
15
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
16

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

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

19. Barcode Gap Analysis
SSU RPB1
LSU ITS
19

20. Pairwise comparisons ITS
(2972 strains)
20

21. PCR Success
21

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 family
22

23. What comes next? Secondary markers
• Penicillium
– ITS, -tubulin
• Trichoderma
– ITS, TEF1
• Fusarium
– TEF1, RPB1, RPB2
Trichoderma spirale

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.
Rosling et 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
Bactridium flavum Sphaerosporium lignitile