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Session 2 Non-COI Candidate regions John Taylor Tom Bruns Sung-Oui Suh François Lutzoni Dirk Redecker Todd DeSantis Teun Boekhout Barbara Robbertse Irina Druzhinina. Fungal Barcoding. John W. Taylor University of California Berkeley, USA. Barcoding fungi is a great idea.

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Session 2

Non-COI Candidate regions

John Taylor

Tom Bruns

Sung-Oui Suh

François Lutzoni

Dirk Redecker

Todd DeSantis

Teun Boekhout

Barbara Robbertse

Irina Druzhinina


Fungal Barcoding

John W. Taylor

University of California

Berkeley, USA


Barcoding fungi is a great idea.

The potential benefits for fungi are huge because most fungi are microscopic and we believe that most are unknown.

Ecology and its applications would benefit tremendously.

http://www.barcode.it/


Barcoding fungi is a great idea.

The potential benefits for fungi are huge because most fungi are microscopic and we believe that most are unknown.

Ecology and its applications would benefit tremendously.

http://www.barcode.it/


Barcoding fungi is a great idea.

The potential benefits for fungi are huge because most fungi are microscopic and we believe that most are unknown.

Ecology and its applications would benefit tremendously.

http://www.barcode.it/


Cytochrome Oxidase I

is not the right gene for fungal barcoding.

From the barcoding website:

http://www.dnabarcoding.ca/primer/Primers.html

PRIMERS Overview In order to obtain barcode sequences from such a broad spectrum of animal taxa, researchers require an arsenal of primer sets.


Cytochrome Oxidase I

is not the right gene for fungal barcoding.

From the barcoding website:

http://www.dnabarcoding.ca/primer/Primers.html

PRIMERS Overview In order to obtain barcode sequences from such a broad spectrum of animal taxa, researchers require an arsenal of primer sets.


If Cytochrome Oxidase I requires an arsenal of primers, how can it work for any group of organisms?


Macrobes v. Microbes can it work for any group of organisms?

Macrobes: Phenotype is available in museums or herbaria, zoos or gardens, and nature. Taxa are well sampled.

Microbes: Phenotype is available in herbaria and culture collections but NOT in nature. Taxa are poorly sampled.


www.livescience.com can it work for any group of organisms?

Ward et al. (2005) amplified COI from more than 200 fish

using different combinations of four newly designed primers:

FishF1-50TCAACCAACCACAAAGACATTGGCAC30,

FishF2-50TCGACTAATCATAAAGATATCGGCAC30,

FishR1-50TAGACTTCTGGGTGGCCAAAGAATCA30,

FishR2-50ACTTCAGGGTGACCGAAGAATCAGAA30.

However, there was insufficient product from five species,

necessitating the use of an additional forward primer:

(50ATCTTTGGTGCATGAGCAGGAATAGT30)


Ward et al. (2005) can it work for any group of organisms? amplified COI from more than 200 fish

using different combinations of four newly designed primers:

FishF1-50TCAACCAACCACAAAGACATTGGCAC30,

FishF2-50TCGACTAATCATAAAGATATCGGCAC30,

FishR1-50TAGACTTCTGGGTGGCCAAAGAATCA30,

FishR2-50ACTTCAGGGTGACCGAAGAATCAGAA30.

However, there was insufficient product from five species,

necessitating the use of an additional forward primer:

(50ATCTTTGGTGCATGAGCAGGAATAGT30)

FIVE PRIMERS FOR FISH


Figure 3 can it work for any group of organisms?


Figure 3 can it work for any group of organisms?


Figure 3 can it work for any group of organisms?


http://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Mouldshttp://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds

Seifert et al. (2007). We tested the performance of PenF1 with

both PenR1 and AspR1 in PCR amplifications using genomic

DNA isolated from ten species of the family Trichocomaceae,

PCR amplications using PenF1 and PenR1 were sporadically

successful, whereas amplications using AspR1 had a 100%

success rate.

Aspergillus and Penicillium subgenus Penicillium are closer

relatives than either is to Penicillium subgenus Biverticillium.


Seifert et al. 2007http://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds


Newhttp://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds

Fungi

In

Tundra

Soils

Schadt et al. 2003


Newhttp://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds

Fungi

In

Tundra

Soils

Schadt et al. 2003


Newhttp://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds

Fungi

In

Tundra

Soils

rDNA sequences

Schadt et al. 2003


Thankshttp://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds


Session 2 http://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds

Non-COI Candidate regions

John Taylor

Tom Bruns

Sung-Oui Suh

François Lutzoni

Dirk Redecker

Todd DeSantis

Teun Boekhout

Barbara Robbertse

Irina Druzhinina


Barcoding Decapods (Crustacea) Costa et al. 2007http://www.botany.utoronto.ca/ResearchLabs/MallochLab/Malloch/Moulds

Forward primers: LCO1490 Crust F1 and Crust F2 (Costa et al. 2007).

Reverse primer: HCO2198 (Folmer et al. 1994).


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