Establishing standards for barcoding and highlighting some of the problems with inconsistencies within the barcode library.

1. lnformatics Workshop, Adelaide 28 November 2011
The BARCODE Data Standard:
Enabling Molecular Diagnostics
for Biodivesity
Robert Hanner, Ph.D.
Centre for Biodiversity Genomics
University of Guelph, Canada

2. The Infrastructure of Taxonomy
Collections and databases of specimens
Codes of Taxonomic Nomenclature
Compilations of taxonomic names
Monographs
Floristic and faunistic surveys/inventories
Revisions
The (undigitized) Taxonomic Literature

4. DNA Barcoding New tools for taxonomy
The ability to compare genotype
information across a huge range of
organisms is a powerful tool

5. Emerging Applications

6. Couplets Consisting of:
“Species Name - DNA Sequence”
Basis of a “look-up table” enabling
molecular diagnostic applications
However, both elements are assertions
Underlying specimens and associated
raw sequence data are not typically
available for secondary inspection

8. Manual Assembly
Subjective interpretation?

9. “Only [27%] of papers had a legitimate specimens
examined section, with museum numbers for each
voucher, and names of the museums where the
specimens used in the study could be examined”

10. Problem Areas
TRANSPARENCY AND TRACEABILITY
Genetic Data Quality
Specimen Data Quality
Taxonomy
Information Access

11. First International
Barcode of Life Conference

12. Barcoders began calling for a Paradigm Shift

13. Barcoding:
Integrating Best Practices
Genomics
Classical
Taxonomy

14. Data Standards for BARCODE
Records in INSDC*
Community-based standards for COI
Creation of a reserved keyword BARCODE
- Required & recommended data elements
- Sequence quality and coverage
Recommended for identifying unknowns
Process to propose non-COI gene regions
*http://barcoding.si.edu/pdf/dwg_data_standards-final.pdf

15. Second International Barcode of
Life Conference 17-21 Sept 2007

17. Validation demonstrates that a procedure is
robust, reliable and reproducible.
PCR amplification and DNA sequencing:
• Are robust methods which produces
successful results a high percentage of the
time.
• Are reliable methods that produce accurate
results.
• Are reproducible methods producing similar
results each time a sample is tested.

18. Third International
Barcode of Life Conference

19. 2009: Barcode Markers for Plants
52 authors from 24 institutions in 9
nations, proposed a pair of short
sequences (totaling about 1,450 base
pairs) from rbcL and matK as the
foundation for a DNA barcode library for
plants.
CBOL Plant Working Group (2009) A DNA barcode for
land plants. Proc Natl Acad Sci USA 106:12794–12797.

20. Fourth International
Barcode of Life Conference

21. 2011: Barcode Marker for Fungi
149 authors from 71 institutions propose
ITS as fungal barcode target. It also has
demonstrated utility in some plants*.
Fungal Barcoding Consortium (2011) The nuclear
ribosomal internal transcribed spacer (ITS) region as a
universal DNA barcode marker for Fungi. Proc Natl Acad
Sci USA (Submitted).
*Hollingsworth (2011) Refining the DNA barcode for land
plants. www.pnas.org/cgi/doi/10.1073/pnas.1116812108

22. Move toward rapid data release:
In 2009 the community acknowledged
the value of the “Ft Lauderdale Accord”
Raw sequence data and high-level
taxonomy (eg order) deposited in INSDC
prior to publication
Gave rise to “Dark taxa” in INSDC and
subsequent arguments pro & con

23. Issues that need to be addressed:
Legacy BARCODE records lack trace
files
Many recent BARCODE records lack
valid names
Not all potential BARCODE data is in the
public domain

24. Question: What is barcoding?
A method for species identification and
discovery through the analysis of short,
standardized DNA sequences
Should BARCODE be applied only to
known species as an ID tag, or should it
be used to designate a sequence entry
conforming to a meta-data standard?

25. DNA Barcodes: a tool of integrative taxonomy
DNA Identification DNA Taxonomy
Barcoding
Low ambiguity High ambiguity
Species well-known Species unknown

26. Evolution of Standards
Even among well-studied vertebrates:
serious discrepancies exist in the
application of names across labs
Identification accuracy of reference
collections highly variable
Perhaps BARCODE is a better process
tag unless reserved for published data

27. 2011: BOLD 3.0
Supports assembly of BARCODE
compliant data records for all markers
Includes specimen images and
introduces BINs to aid data validation
Introduces features for 3rd party
annotation of data records to facilitate
library curation

28. What other issues remain?
Barcode annotation of plants and fungi?
Registration of institutions/collections
Synchronization of data bases

29. www.biorepositories.org

30. Structured Reference to Vouchers?

31. LinkOut to Collection Catalogs

32. Accomplishments:
Integration of genomics and biodiversity
science via creation of a robust molecular
diagnostic interface between them
Increased community awareness of
taxonomy and collections

33. Acknowledgments:
 All Participants of the CBOL Database Work
Group and many, many others!

34. Rationale for Defining
“BARCODE” keyword in GenBank
Provides the community with reference
records with verifiable and retrievable data:
 Associated with retrievable voucher specimens
(liberally defined: tissue, DNA, etc.)
 Linked to on-line metadata
 Meet an agreed upon standard of taxonomic
identification
 Provide an assured level of data completeness
 On an agreed upon gene region
 Recommended for use in identifying unknowns

35. The Barcode Data Standard
Establishing a new data standard for “BARCODE”
keyword records in DDBJ/EMBL/GenBank:
1. Minimum 500bp, <1% ambiguous base calls
2. Double stranded sequence
3. Trace files and associated quality scores
4. Primers used to generate sequence
5. Linkages to:
1. A morphological voucher specimen
2. Structured reference to collections
3. Geospatial reference information
4. Valid species name
5. Who performed the identification
6. Literature citations

36. BARCODE Records (without trace files)