Plant Barcoding

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Plant Barcoding

  1. 1. DNA barcoding and the CBOL plant working group Pete Hollingsworth Royal Botanic Garden Edinburgh
  2. 2. Talk Overview • Selecting a plant barcode • Current plant barcoding activities
  3. 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. 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. 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. 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. 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. 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. 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. 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. 11. PLANT DIVERSITY
  12. 12. PLANT LAND PLANTS • c. 400,000 species DIVERSITY VASCULAR PLANTS • > 350,000 species • c. 13,888 genera • c. 511 families
  13. 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. 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. 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. 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. 17. DNA barcoding in the Forest Dynamics Plot on Barro Colorado Island (BCI), Panama Kress et al. (2009) PNAS 106: 18621-18626
  18. 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. 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

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