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)