Dr Robert Hanner - Barcode Data standards for animals, plants & fungi
lnformatics Workshop, Adelaide 28 November 2011 The BARCODE Data Standard: Enabling Molecular Diagnostics for BiodivesityRobert Hanner, Ph.D.Centre for Biodiversity GenomicsUniversity of Guelph, Canada
The Infrastructure of TaxonomyCollections and databases of specimensCodes of Taxonomic NomenclatureCompilations of taxonomic namesMonographsFloristic and faunistic surveys/inventoriesRevisionsThe (undigitized) Taxonomic Literature
DNA Barcoding New tools for taxonomy The ability to compare genotype information across a huge range of organisms is a powerful tool
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
Barcoding: Integrating Best Practices Genomics Classical Taxonomy
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 ofLife 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.
2009: Barcode Markers for Plants52 authors from 24 institutions in 9nations, proposed a pair of shortsequences (totaling about 1,450 basepairs) from rbcL and matK as thefoundation for a DNA barcode library forplants.CBOL Plant Working Group (2009) A DNA barcode forland plants. Proc Natl Acad Sci USA 106:12794–12797.
Fourth InternationalBarcode of Life Conference
2011: Barcode Marker for Fungi149 authors from 71 institutions proposeITS as fungal barcode target. It also hasdemonstrated utility in some plants*.Fungal Barcoding Consortium (2011) The nuclearribosomal internal transcribed spacer (ITS) region as auniversal DNA barcode marker for Fungi. Proc Natl AcadSci USA (Submitted).*Hollingsworth (2011) Refining the DNA barcode for landplants. 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 publicationGave rise to “Dark taxa” in INSDC and subsequent arguments pro & con
Issues that need to be addressed:Legacy BARCODE records lack trace filesMany recent BARCODE records lack valid namesNot 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 sequencesShould 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?
DNA Barcodes: a tool of integrative taxonomy DNA Identification DNA Taxonomy BarcodingLow ambiguity High ambiguitySpecies well-known Species unknown
Evolution of StandardsEven 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 3.0Supports assembly of BARCODE compliant data records for all markersIncludes specimen images and introduces BINs to aid data validationIntroduces 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
Accomplishments:Integration of genomics and biodiversity science via creation of a robust molecular diagnostic interface between themIncreased 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 GenBankProvides 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
The Barcode Data StandardEstablishing 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 specimen 2. Structured reference to collections 3. Geospatial reference information 4. Valid species name 5. Who performed the identification 6. Literature citations