Test test

1. DNA barcoding and the CBOL plant
working group
Pete Hollingsworth
Royal Botanic Garden Edinburgh

2. Talk Overview
• Selecting a plant barcode
• Current plant barcoding activities

3. Choosing a plant barcode
• 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…..

4. ITS trnH-psbA rbcL rpoC1 rpoB matK ycf5 accD ndhJ atpF-H psbK-I
2005
(1st BoL Kress Chase et al.
Meeting) et al.
Kew consortium project
Newmaster
et al.
2006
Partial
rbcL
2007
Kress +
Erickson
Kim et al.
2nd BoL meeting
2008

5. ITS trnH-psbA rbcL rpoC1 rpoB matK ycf5 accD ndhJ atpF-H psbK-I
2005
(1st BoL Kress Chase et al.
Meeting) et al.
Kew consortium project
Newmaster
et al.
2006
Partial
rbcL
2007 Kress +
Kress +
Erickson
Erickson
Kim et al.
2nd BoL meeting
2008

6. 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

7. 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

8. Selection of a plant barcode
• 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
Recommendation accepted by CBOL

9. % Discrimination success
• 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”
80%
70%
60%
50%
40%
1 locus 2 locus 3 locus

10. 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

11. PLANT
DIVERSITY

12. PLANT
LAND PLANTS
• c. 400,000 species DIVERSITY
VASCULAR PLANTS
• > 350,000 species
• c. 13,888 genera
• c. 511 families

13. 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

14. What is a tree? International collaborative plant barcoding project
Ultimate goal is to barcode all 100K tree species
A plant that would hurt you if you ran into it

15. GrassBOL
An international initiative to barcode the grasses of the world
• Ecologically and economically important
• Difficult to identify
• Model system to develop
plant barcoding protocols
Andy Lowe Hugh Cross Sean Graham
Adelaide University & University of British Columbia
State Herbarium of South Australia

16. Center for Tropical Forest Science
Smithsonian Institution Global Earth
Observatories (SIGEO)
Smithsonian Tropical Research Institute
Center for Tropical Forest Science
**
*
* ***
Smithsonian Institution Global Earth Observatories
* (SIGEO) *
* *
* **
A global program of long-term forest research: monitoring
*
the impact of climate change
Purpose:
*Forest Dynamics
*Climate Change
Expanding the network!
*Conservation

17. DNA barcoding in the Forest
Dynamics Plot on Barro
Colorado Island (BCI), Panama
Kress et al. (2009) PNAS 106:
18621-18626

18. 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

19. Acknowledgements
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
RBGE Strategic Review November 2009