Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials
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...
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| creator | Meiklejohn, Kelly A Damaso, Natalie Robertson, James M |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0217084 |
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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. 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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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>31216285</pmid><doi>10.1371/journal.pone.0217084</doi><tpages>e0217084</tpages><orcidid>https://orcid.org/0000-0001-6125-2963</orcidid><orcidid>https://orcid.org/0000000161252963</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2019-06, Vol.14 (6), p.e0217084-e0217084 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2243464363 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Accident prevention Accuracy Animals Bar codes BASIC BIOLOGICAL SCIENCES Biological evolution Biological materials Biology and Life Sciences Computer and Information Sciences Counterterrorism Criminal investigation Cytochrome Data bases Databases, Nucleic Acid Deoxyribonucleic acid DNA DNA barcoding DNA Barcoding, Taxonomic - methods Evolutionary biology Explosions Forensic science Forensic sciences Fungi Fungi - classification Fungi - genetics Gene sequencing Genes Genetic research Genomes Identification Insecta - classification Insecta - genetics Insects Laboratories Morphology Nucleotide sequence Plants - classification Plants - genetics Quality Reference materials Regulatory compliance Reliability analysis Repositories Reproducibility of Results Research and Analysis Methods Ribosomal RNA Science & Technology - Other Topics Taxonomy |
| title | Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-16T17%3A09%3A17IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Assessment%20of%20BOLD%20and%20GenBank%20-%20Their%20accuracy%20and%20reliability%20for%20the%20identification%20of%20biological%20materials&rft.jtitle=PloS%20one&rft.au=Meiklejohn,%20Kelly%20A&rft.aucorp=Federal%20Bureau%20of%20Investigation%20(FBI)%20Lab.%20Division,%20Quantico,%20VA%20(United%20States).%20Counterterrorism%20and%20Forensic%20Science%20Research%20Unit&rft.date=2019-06-19&rft.volume=14&rft.issue=6&rft.spage=e0217084&rft.epage=e0217084&rft.pages=e0217084-e0217084&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0217084&rft_dat=%3Cgale_plos_%3EA589744674%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2243464363&rft_id=info:pmid/31216285&rft_galeid=A589744674&rft_doaj_id=oai_doaj_org_article_3e90be41b1c7470dbd622fed81eb9c13&rfr_iscdi=true |