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An Official Barcode for Fungi. Conrad Schoch Keith Seifert John Spouge Vincent Robert Elena Bolchacova Pedro Crous , &…. and a cast of thousands… (…or more than 140 collaborators from 20 countries).

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slide1

An Official Barcode for Fungi

Conrad Schoch

Keith Seifert

John Spouge

Vincent Robert

Elena Bolchacova

Pedro Crous,

&…

slide2

and a cast of thousands…

(…or more than 140 collaborators from 20 countries)

slide3

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

slide4

‘true’ Fungi

Keeling et al.2005

Fungi within Eukaryotes

slide5

Ascomycota

Basidiomycota

Glomeromycota

FUNGI

‘early diverging’ lineages

zygomycetes,

chytrids,

Microsporidia

Oomycetes

Green plants

From James et al., Nature 2006

0.2

slide6

Ascomycotanvs Chordate diversity

Subphylum:Saccharomycotina

Phylum:Chordata

The Scientist

the fate of cox1 for fungal barcoding

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

slide9

http://www.fungalbarcoding.org

Vincent Robert

Biolomics & CBS

slide11

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

slide12

Ascomycota

Elena Bolchacova

LifeTech

Basidiomycota

slide13

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

slide14

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

slide15

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

slide16

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

slide17

Combined 4 gene comparison

(746 strains, 396 spp)

SSU

RPB1

LSU

ITS

slide18

Combined 6 gene comparison

(207 strains, 55 species)

SSU

RPB2

RPB1

MCM7

LSU

ITS

slide22

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
what comes next secondary markers
What comes next? Secondary markers

Penicillium

ITS, -tubulin

Trichoderma

ITS, TEF1

Fusarium

TEF1, RPB1, RPB2

Trichodermaspirale

slide24

JGI Community Sequencing Program

1000 fungal genomes over

5 years

Where does barcoding fit?

what else is out there
What else is out there?

Cryptomycota

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

Roslinget al. 2011. Science 333: 876-879.

environmental diversity real or virtual species
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
We need to become more efficient (and better) at describing fungal diversity

Two commonly found Fungi – no sequence data, no cultures

BactridiumflavumSphaerosporiumlignitile