Conrad Schoch - Saturday Closing Plenary

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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

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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1111

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

1313

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)

1818

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

2020

Pairwise comparisons ITS (2972 strains)

Pairwise comparisons ITS (2972 strains)

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PCR SuccessPCR Success

2222

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

What comes next? Secondary markers

• Penicillium– ITS, -tubulin

• Trichoderma – ITS, TEF1

• Fusarium – TEF1, RPB1, RPB2

Trichoderma spirale

JGI Community Sequencing Program

1000 fungal genomes over

5 years

Where does barcoding fit?

What else is out there?

Jones et al. 2011. Nature 474: 200-203.

Rosling et al. 2011. Science 333: 876-879.

Cryptomycota

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 diversity

Two commonly found Fungi – no sequence data, no cultures Bactridium flavum Sphaerosporium lignitile