Abstract

Introduction:  Chacón-Monge et al. (2024) sought to test the accuracy of DNA barcoding for species identification in Pacific Central American shallow water echinoderms. They used cytochrome c oxidase I (COI) sequences derived from new material collected as part of the BioMar-ACG project in Costa Rica. Using their set of 348 echinoderm sequences, they compared species identification results from two online platforms: the National Center for Biotechnology Information (NCBI) GenBank using the nucleotide Basic Local Alignment Search Tool (BLASTn), and the Barcode of Life Data Systems (BOLD) Identification Engine.

Objective:  The present article is a response to their results and conclusions.

Methods:  We reinterpreted the results from the authors’ Appendix 2 to enable an objective comparison between the BOLD Identification Engine and BLASTn in GenBank.

Results:  While the authors found that both platforms were limited by the number of reference sequences available in their respective databases, they concluded that GenBank outperformed BOLD for identification; however, we identify several methodological flaws in their analysis. These include pseudoreplication amongst query sequences, contaminated sequences stemming from sampling errors, and a lack of standardization when interpreting results from the two platforms. Their assessment of the BOLD Identification Engine was also limited by improper selection of a reference database.

Conclusion:  Addressing these errors, we reinterpret their results and demonstrate that there is no difference in performance between the two platforms.

Key words: BOLD; GenBank; BLASTn; mitochondrial DNA; sequencing errors; Costa Rica.