Assessment of BOLD and GenBank – Their accuracy and reliability for the identification of biological materials

Meiklejohn, Kelly A.; Damaso, Natalie; Robertson, James M.

doi:10.1371/journal.pone.0217084

Title: Assessment of BOLD and GenBank – Their accuracy and reliability for the identification of biological materials

Journal Article · 19 June 2019 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0217084 · OSTI ID:1627883

^[1]; Damaso, Natalie ^[1]; Robertson, James M. ^[1]

Federal Bureau of Investigation (FBI) Lab. Division, Quantico, VA (United States). Counterterrorism and Forensic Science Research Unit

Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown “barcode” sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.

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Research Organization:: Federal Bureau of Investigation (FBI) Lab. Division, Quantico, VA (United States). Counterterrorism and Forensic Science Research Unit

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 1627883

Journal Information:: PLoS ONE, Vol. 14, Issue 6; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 116 works

Citation information provided by
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S4 Table: Specimen information and barcode results for plants. Meiklejohn, Kelly A.; Damaso, Natalie; Robertson, James M. figshare https://doi.org/10.6084/m9.figshare.8182703	dataset	January 2020
S2 Table: Specimen information and barcode results for insects Meiklejohn, Kelly A.; Damaso, Natalie; Robertson, James M. figshare https://doi.org/10.6084/m9.figshare.8182631.v1	dataset	January 2020
S3 Table. Specimen information and barcode results for macro-fungi. Meiklejohn, Kelly A.; Damaso, Natalie figshare https://doi.org/10.6084/m9.figshare.8182700.v1	dataset	January 2020
S4 Table: Specimen information and barcode results for plants. Meiklejohn, Kelly A.; Damaso, Natalie; Robertson, James M. figshare https://doi.org/10.6084/m9.figshare.8182703.v1	dataset	January 2020
S1 File. BOLD and GenBank output for samples used in statistical analyses (insects, n=17; macro-fungi, n=14; plants 2-loci, n=53; plants 4-loci, n=28). Meiklejohn, Kelly A.; Damaso, Natalie; Robertson, James M. figshare https://doi.org/10.6084/m9.figshare.8183063	dataset	January 2020
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Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants Wilkinson, Mike J.; Szabo, Claudia; Ford, Caroline S. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep46040	journal	April 2017
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GenBank Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1094	journal	November 2017
Biological identifications through DNA barcodes Hebert, Paul D. N.; Cywinska, Alina; Ball, Shelley L. Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 270, Issue 1512 https://doi.org/10.1098/rspb.2002.2218	journal	February 2003
Plant DNA barcoding: from gene to genome: Plant identification using DNA barcodes Li, Xiwen; Yang, Yang; Henry, Robert J. Biological Reviews, Vol. 90, Issue 1 https://doi.org/10.1111/brv.12104	journal	March 2014
Using COI barcodes to identify forensically and medically important blowflies Nelson, L. A.; Wallman, J. F.; Dowton, M. Medical and Veterinary Entomology, Vol. 21, Issue 1 https://doi.org/10.1111/j.1365-2915.2007.00664.x	journal	March 2007
An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity Ryberg, Martin; Kristiansson, Erik; Sjökvist, Elisabet New Phytologist, Vol. 181, Issue 2 https://doi.org/10.1111/j.1469-8137.2008.02667.x	journal	November 2008
Where are all the undocumented fungal species? A study of Mortierella demonstrates the need for sequence-based classification: Commentary Hibbett, David; Glotzer, Dylan New Phytologist, Vol. 191, Issue 3 https://doi.org/10.1111/j.1469-8137.2011.03819.x	journal	July 2011
Protax -fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences Abarenkov, Kessy; Somervuo, Panu; Nilsson, R. Henrik New Phytologist, Vol. 220, Issue 2 https://doi.org/10.1111/nph.15301	journal	July 2018
Application of DNA-Based Methods in Forensic Entomology Wells, Jeffrey D.; Stevens, Jamie R. Annual Review of Entomology, Vol. 53, Issue 1 https://doi.org/10.1146/annurev.ento.52.110405.091423	journal	January 2008
Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family Gao, Ting; Yao, Hui; Song, Jingyuan BMC Evolutionary Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2148-10-324	journal	October 2010
Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective Nilsson, R. Henrik; Ryberg, Martin; Kristiansson, Erik PLoS ONE, Vol. 1, Issue 1 https://doi.org/10.1371/journal.pone.0000059	journal	December 2006
Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species Chen, Shilin; Yao, Hui; Han, Jianping PLoS ONE, Vol. 5, Issue 1 https://doi.org/10.1371/journal.pone.0008613	journal	January 2010
Barcoding Beetles: A Regional Survey of 1872 Species Reveals High Identification Success and Unusually Deep Interspecific Divergences Pentinsaari, Mikko; Hebert, Paul D. N.; Mutanen, Marko PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0108651	journal	September 2014
Testing DNA Barcode Performance in 1000 Species of European Lepidoptera: Large Geographic Distances Have Small Genetic Impacts Huemer, Peter; Mutanen, Marko; Sefc, Kristina M. PLoS ONE, Vol. 9, Issue 12 https://doi.org/10.1371/journal.pone.0115774	journal	December 2014
Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger Macher, Jan-Niklas; Macher, Till-Hendrik; Leese, Florian Metabarcoding and Metagenomics, Vol. 1 https://doi.org/10.3897/mbmg.1.22262	journal	December 2017
Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France Sonet, Gontran; Jordaens, Kurt; Braet, Yves ZooKeys, Vol. 365 https://doi.org/10.3897/zookeys.365.6027	journal	December 2013
S1 Table. Primers and thermal cycling conditions used to amplify each barcoding region for insects, macro-fungi, and plants. Meiklejohn, Kelly A.; Damaso, Natalie; Robertson, James M. figshare https://doi.org/10.6084/m9.figshare.8171147	dataset	January 2020

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