Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials - PubMed (original) (raw)

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

Kelly A Meiklejohn et al. PLoS One. 2019.

Abstract

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.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1

Fig 1

Overall classification accuracies from BOLD and GenBank for: A) COI insect sequences (n = 17), B) ITS macro-fungi sequences (n = 14), and C) plant taxa using either a 2-locus (rbcL and matK; n = 53) and 4-locus approach (rbcL, matK, trnH-psbA and ITS2; n = 28). The identification success for genus is denoted by the light color and species by the dark color. Blue bars correspond to results from searches against BOLD and green against GenBank.

Fig 2

Fig 2

Classification using BOLD and GenBank for: A-B) COI insect sequences (n = 17), C-D) ITS macro-fungi sequences (n = 14), and E-F) plant taxa using either a 2-locus approach (rbcL and matK; n = 53) or 4-locus approach (rbcL, matK, trnH-psbA, and ITS2; n = 28). A,C,E) Assessment of the specificity of the top match(es) in both databases: reliable match, where all records with the same top match statistics matched the expected taxa (dark blue), or ambiguous match, where records with the same top statistic match represent more than one species (other colors; e.g., gray = undetermined species, light blue = congeneric species, etc). B,D,F) Taxonomic level classification. Taxa were correctly identified to the species-level (dark blue) or higher taxonomic level (other colors; e.g., light blue = genus, green = class, etc).

Similar articles

Cited by

References

    1. Bruns TD, White TJ, & Taylor JW. Fungal molecular systematics. Annu. Rev. Ecol. Syst. 1991;22: 525–564.
    1. Hebert PD, Cywinska A, Ball SL, & Dewaard JR. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. Series B: Biol. Sci. 2003;270: 313–321. - PMC - PubMed
    1. Group CPW, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, et al. A DNA barcode for land plants. PNAS. 2009;106: 12794–12797. 10.1073/pnas.0905845106 - DOI - PMC - PubMed
    1. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS. 2012;109: 6241–6246. 10.1073/pnas.1117018109 - DOI - PMC - PubMed
    1. Ratnasingham S, & Hebert PD. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Resour. 2007;7: 355–364. - PMC - PubMed

Publication types

MeSH terms

Grants and funding

This research was supported in part by an appointment to the Visiting Scientist Program at the FBI Laboratory Division, administered by the Oak Ridge Institute of Science and Education, through an interagency agreement between the US Department of Energy and the FBI. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

LinkOut - more resources