DNA barcoding and the CBOL plant

working group

Pete Hollingsworth

Royal Botanic Garden Edinburgh

Talk Overview• Selecting a plant barcode

• Current plant barcoding activities

• CO1

– Single locus with high discriminatory power

– Coding

• enables translation to check sequence reads

– Alignable

• facilitates comparative analyses

– Well-developed primer sets

Minimalism, Scalability, Standardisation

• Finding the plant equivalent…..

Choosing a plant barcode

ITS trnH-psbA rbcL rpoC1 rpoB matK ycf5 accD ndhJ atpF-H

Kim et al.

2nd BoL meeting

Kress

et al.

Chase et al.

Partial

rbcL

Kress +

Erickson

Newmaster

et al.

Kew consortium project

psbK-I

2005

2006

2007

2008

(1st BoL

Meeting)

ITS trnH-psbA rbcL rpoC1 rpoB matK ycf5 accD ndhJ

2005

2006

2007

2008

Kress

et al.

Chase et al.

Kress +

Erickson

(1st BoL

Meeting)

Newmaster

et al.

Kew consortium project

Partial

rbcL

Kress +

Erickson

atpF-H

Kim et al.

2nd BoL meeting

psbK-I

Selecting the plant barcode

• Collaboration to recommend a standard plant barcode (among research groups who had compared all 7 loci)

• Pool data on the 7 candidate loci (plastid regions)

• Analyses of data

• Discussions

Evaluation of 7

candidate barcodes

against three criteria:

Universality: Is it easy to

obtain sequences?

Sequence quality: Are the

sequence traces unambiguous

and are bidirectional reads

obtained?

Discriminatory power: Is it

good at telling species apart?

CBOL Plant Working Group (2009) A DNA barcode for land

plants. Proceedings of the National Academy of Sciences,

USA, 106: 12794-12797

• From 7 plastid loci, 3 were short-listed– rbcL easy to use, but modest discriminatory power

– matK higher discrimination and coding (closest to CO1), but lower universality

– trnH-psbA good universality, higher discrimination, but length variable and frequent termination of sequencing reads by SSRs

• Selecting a barcode from these loci was a close call, and there is no perfect solution

• Majority recommendation of a core-barcode of two coding genes: rbcL + matK

Selection of a plant barcode

Recommendation accepted by CBOL

% Discrimination success

1 locus 2 locus 3 locus

80%

70%

60%

50%

40%

• Adding >2 plastid loci on average leads to diminishing returns of

discrimination

• Species discrimination asymptotes at ca 70-75%

Remaining species identified to “species groups”

Challenges

• Primer development required to improve amplification and sequencing success of matK

• Supplementary loci will be required to increase discriminatory power

• Review rbcL+matK barcode after 18 months (recommendation by CBOL)– Assess amplification and sequencing success for matK

– Encourage further sequencing/assessment of supplementary barcodes such as trnH-psbA and ITS during this period

PLANT

DIVERSITY

LAND PLANTS• c. 400,000 species

VASCULAR PLANTS

• > 350,000 species

• c. 13,888 genera

• c. 511 families

PLANT

DIVERSITY

Plant Working Group meeting

• Sampling strategies

• Tissue storage

• Barcode protocol

development

– Primer developments

– Opportunities for increasing

discriminatory power

– Improvements in sequencing

protocols

• Overview of plant barcoding projects

International collaborative plant barcoding project

Ultimate goal is to barcode all 100K tree species

What is a tree?

A plant that would hurt you if you ran into it

An international initiative to barcode the grasses of the world

GrassBOL

• Ecologically and economically important

• Difficult to identify

• Model system to develop

plant barcoding protocols

Andy Lowe Sean GrahamHugh Cross

Adelaide University &

State Herbarium of South AustraliaUniversity of British Columbia

Expanding the network!

Smithsonian Institution Global Earth Observatories(SIGEO)

A global program of long-term forest research: monitoring the impact of climate change

Smithsonian Tropical Research Institute

Center for Tropical Forest Science

Center for Tropical Forest ScienceSmithsonian Institution Global Earth

Observatories (SIGEO)

**

**

*

**

**

*

*

Purpose:

*Forest Dynamics*Climate Change*Conservation

*

*

**

Kress et al. (2009) PNAS 106:

18621-18626

DNA barcoding in the Forest

Dynamics Plot on Barro

Colorado Island (BCI), Panama

Plant Barcode of Life in China

• Major grant from Chinese Academy of Sciences

• Three year plant barcoding project

• De-Zhu Li (Kunming Institute of Botany)

• 51 research groups from 14 institutes

RBGE Strategic Review November 2009

CBOL Plant Working Group

The Alfred P. Sloan Foundation, Gordon and Betty Moore Foundation, Genome Canada, Scottish

Government’s Rural and Environment Research and Analysis Directorate, CAS, NSF, Intramural

Research Program of the National Library of Medicine, Tupper post-doctoral fellowship, and CBOL

Acknowledgements