conrad schoch - saturday closing plenary
TRANSCRIPT
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Conrad SchochKeith SeifertJohn SpougeVincent RobertElena BolchacovaPedro Crous,&…
An Official Barcode for Fungi
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and a cast of thousands… (…or more than 140 collaborators from 20 countries)
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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
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Fungi within EukaryotesKeeling et al. 2005
‘true’ Fungi
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FU
NG
I
0.2From James et al., Nature 2006
Oomycetes
‘early diverging’ lineages
zygomycetes, chytrids,
Microsporidia
Ascomycota
Basidiomycota
Glomeromycota
Green plants
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Ascomycotan vs Chordate diversityP
hylu
m:C
hord
ata
Su
bp
hylu
m:S
acch
aro
mycoti
na
The Scientist
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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
Barcode
Zasmidium nocoxi Crous
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Fungal DNA barcoding workshop Amsterdam April 2011
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http://www.fungalbarcoding.org
Vincent RobertBiolomics & CBS
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1010
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Genes:ITSLSUSSURPB1
RPB2MCM7
Pezizomycotina
Saccharomycotina
Taphrinomycotina
UstilaginomycotinaAgaricomycotina
Pucciniomycotina
Glomeromycota
Mortierellomycotina
Kickxellomycotina
Zoopagomycotina
Mucoromycotina
Entomophthoromycotina
ChytridiomycotaNeocallimastigomycota
BlastocladiomycotaMicrosporidiarozellid clade
Nucleariida
Mesomycetozoa
Ascomycota
Basidiomycota
Dikarya
Fungi
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Elena BolchacovaLifeTech
Ascomycota
Basidiomycota
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Pezizomycotina
Saccharomycotina
Taphrinomycotina
UstilaginomycotinaAgaricomycotina
Pucciniomycotina
Glomeromycota
Mortierellomycotina
Kickxellomycotina
Zoopagomycotina
Mucoromycotina
Entomophthoromycotina
ChytridiomycotaNeocallimastigomycota
BlastocladiomycotaMicrosporidiarozellid clade
Nucleariida
Mesomycetozoa
John SpougeNCBI
746 strains, 396 speciesDivided into 4 sets4 markers each
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Coverage : Samples in Species
Basidiomycota
B ‘Early diverging’ lineages
Pezizomycotina
49 genera
83 species
140 samples
49 genera
83 species
140 samples
Saccharomycotina
36+13=49 species
85 samples
21+8=29 species
43 samples
49+43=92 species
202 samples
84+142=226 species
416 samples
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The Status of a Species’s Nearest Neighbor List
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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
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
In the dataset, calculate the fraction of species where the nearest neighbor list is correct for every sample
Percent correct identification (PCI)
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Individual PCIs
The fraction of specieswhere the nearest neighbor list is
correct for every sample
Pezizomycotina Basidiomycota Saccharomycotina Early diverging All
S=SSUR=RPB1L=LSUI=ITS
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SSU
RPB1
LSU
ITS
Combined 4 gene comparison(746 strains, 396 spp)
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SSU
RPB2
RPB1
MCM7
LSU
ITS
Combined 6 gene comparison(207 strains, 55 species)
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Barcode Gap AnalysisBarcode Gap Analysis
SSU
LSU
RPB1
ITS
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2020
Pairwise comparisons ITS (2972 strains)
Pairwise comparisons ITS (2972 strains)
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PCR SuccessPCR Success
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Advantages
Universal primers
Large available dataset
Strong demand from espcially ecologists
ITS (Internal Transcribed Spacer) Sequencing(ms. in review at PNAS)
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
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What comes next? Secondary markers
• Penicillium– ITS, -tubulin
• Trichoderma – ITS, TEF1
• Fusarium – TEF1, RPB1, RPB2
Trichoderma spirale
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JGI Community Sequencing Program
1000 fungal genomes over
5 years
Where does barcoding fit?
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What else is out there?
Jones et al. 2011. Nature 474: 200-203.
Rosling et al. 2011. Science 333: 876-879.
Cryptomycota
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Environmental diversity – real or virtual species?
Hibbett et al. 2011. Fungal Biology Reviews 25: 38-47.
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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