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

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.

Gap-analysis of DNA barcoding reference libraries for two taxon inventories

“…Working on reference libraries of DNA barcodes of marine organisms (invertebrates and sh taxa), Weigand et al [5] recorded numerous identi cation errors, sequence contamination, incomplete reference (missing trace les or primer information) as inadequate data management. The results of the present study, as supported by other recent studies [2,5,17,28,30,32], reveal that we are still away from possessing decent representative reference libraries for important taxonomic groups. In addition, new DNA barcode data are continuously made available for the already barcoded and additional species from the reference libraries, including additional auditing and annotation processes, altogether helping in closing gap knowledge and purging accumulated erroneous data.…”

“…The rst indicated that the BINs assignments revealed a sizeable amount of discordances, many are probably related to species misidenti cations or synonyms [28] or the de ciency of the BIN clustering algorithm to correctly discriminate species [30]. The second outcome pointed towards the low power of GenBank results as compared to the BoLD, discrepancies that are already noted in the literature [2,31], characterized by contaminations of the query sequences discordances and misidenti cations. The BoLD and the GenBank data storage systems are highly intermingled.…”

“…The accurate evaluation of the biodiversity for any given ecosystem is a keystone element, even imperative, in numerous biological and applied disciplines, including ecology, conservation biology, food regulatory compliance, forensics, and ecosystem monitoring and assessment [1][2]. In response to the needs, DNA-based taxon identi cation constituted on the Cytochrome Oxidase I (COI) gene are habitually used to assess biodiversity, including species identi cation, species boundaries and species diversity analyses.…”

“…As a curator tool, it is inferred that all barcode sequences stored in the BoLD database are backed by vouchered specimens and thoroughly identi ed by taxonomy experts. Yet, being a public database, it is inevitable that BoLD, as any other similar curation tool, will not accrue erroneous data, sometimes signi cantly [2,6]. Taxonomic misidenti cations and/or taxonomic conundrums, composites of cryptic species complexes, technical faults such as de cient DNA extraction, primary bias and/or PCR-based errors and contaminations by foreign DNA, including bacterial COI sequences, are just part of the causes that may unavoidably generate erroneous data and inaccurate sequences [2,[6][7][8][9][10].…”

A rapid urban biodiversity blitz using aquatic environmental DNA

“…Correct identification of the specimens present in the reference libraries relies heavily on the taxonomic expertise of the researchers, especially for closely-related, morphologically similar taxa. Since the results obtained in this study depend solely on the BOLD database, a certain level of misidentified sequences reflects the BIN discordance observed (Meiklejohn et al, 2019). We have also identified cases where one species comprised more than one BIN.…”