Dr Robert Hanner - Barcode Data standards for animals, plants & fungi
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Transcript of Dr Robert Hanner - Barcode Data standards for animals, plants & fungi
Robert Hanner, Ph.D.Centre for Biodiversity GenomicsUniversity of Guelph, Canada
lnformatics Workshop, Adelaide 28 November 2011
The BARCODE Data Standard: Enabling Molecular Diagnostics
for Biodivesity
The Infrastructure of Taxonomy
Collections and databases of specimensCodes of Taxonomic NomenclatureCompilations of taxonomic namesMonographsFloristic and faunistic surveys/inventoriesRevisionsThe (undigitized) Taxonomic Literature
New tools for taxonomyD
NA
Barc
od
ing
The ability to compare genotype information across a huge range of organisms is a powerful tool
Emerging Applications
Couplets Consisting of:
“Species Name - DNA Sequence”
Basis of a “look-up table” enabling molecular diagnostic applications
However, both elements are assertionsUnderlying specimens and associated raw sequence data are not typically available for secondary inspection
Manual Assembly
Subjective interpretation?
“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”
Problem Areas
TRANSPARENCY AND TRACEABILITY
Genetic Data QualitySpecimen Data QualityTaxonomy Information Access
First International Barcode of Life Conference
Barcoders began calling for a Paradigm Shift
Genomics
Classical Taxonomy
Barcoding: Integrating Best Practices
Data Standards for BARCODE Records in INSDC*
Community-based standards for COICreation of a reserved keyword BARCODE
- Required & recommended data elements
- Sequence quality and coverageRecommended for identifying unknownsProcess to propose non-COI gene regions
*http://barcoding.si.edu/pdf/dwg_data_standards-final.pdf
Second International Barcode of Life Conference 17-21 Sept 2007
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.
Third International Barcode of Life Conference
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.
Fourth International Barcode of Life Conference
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
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
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
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?
BarcodingDNA Taxonomy
DNA Barcodes: a tool of integrative taxonomy
Low ambiguitySpecies well-known
High ambiguitySpecies unknown
DNA Identification
Evolution of Standards
Even among well-studied vertebrates: serious discrepancies exist in the
application of names across labsIdentification accuracy of reference
collections highly variablePerhaps BARCODE is a better process
tag unless reserved for published data
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
What other issues remain?
Barcode annotation of plants and fungi?Registration of institutions/collectionsSynchronization of data bases
www.biorepositories.org
Structured Reference to Vouchers?
LinkOut to Collection Catalogs
Accomplishments:
Integration of genomics and biodiversity science via creation of a robust molecular diagnostic interface between them
Increased community awareness of taxonomy and collections
Acknowledgments:
All Participants of the CBOL Database Work Group and many, many others!
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 metadataMeet an agreed upon standard of taxonomic
identificationProvide an assured level of data completenessOn an agreed upon gene region Recommended for use in identifying unknowns
The Barcode Data Standard
Establishing a new data standard for “BARCODE” keyword records in DDBJ/EMBL/GenBank:
1.Minimum 500bp, <1% ambiguous base calls2.Double stranded sequence3.Trace files and associated quality scores4.Primers used to generate sequence5.Linkages to:
1.A morphological voucher specimen2.Structured reference to collections3.Geospatial reference information4.Valid species name5.Who performed the identification6.Literature citations
BARCODE Records (without trace files)