GenBank is a reliable resource for 21st century biodiversity research

Abstract

Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable. Thus, identifying these sequences typically relies on comparisons with sequences from genetic databases, particularly GenBank. While concerns have been raised about biases and inaccuracies in laboratory and analytical methods, comparatively little attention has been paid to the taxonomic reliability of GenBank itself. Here we analyze the metazoan mitochondrial sequences of GenBank using a combination of distance-based clustering and phylogenetic analysis. Because of their comparatively rapid evolutionary rates and consequent high taxonomic resolution, mitochondrial sequences represent an invaluable resource for the detection of the many small and often undescribed organisms that represent the bulk of animal diversity. We show that metazoan identifications in GenBank are surprisingly accurate, even at low taxonomic levels (likely <1% error rate at the genus level). This stands in contrast to previously voiced concerns based on limited analyses of particular groups and the fact that individual researchers currently submit annotated sequences to GenBank without significant external taxonomic validation. Our encouraging results suggest that the rapid uptake of DNA-based approaches is supported by a bioinformatic infrastructure capable of assessing both the losses to biodiversity caused by global change and the effectiveness of conservation efforts aimed at slowing or reversing these losses.

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

“…Reference databases are crucial to secure taxonomic assignment for data derived from eDNA samples (Zinger et al, 2019). While recent analyses on the taxonomic annotation of metazoan GenBank sequences suggest their reliability for eDNA metabarcoding studies (Leray, Knowlton, Ho, Nguyen, & Machida, 2019; Li et al, 2018), we encountered the need of including a thorough curation step for our ‘global’ database giving several mislabelled sequences. Species-level annotations were not considered in Leray et al (2019), and we found incorrectly annotated sequences at all taxonomic levels.…”

“…While recent analyses on the taxonomic annotation of metazoan GenBank sequences suggest their reliability for eDNA metabarcoding studies (Leray, Knowlton, Ho, Nguyen, & Machida, 2019; Li et al, 2018), we encountered the need of including a thorough curation step for our ‘global’ database giving several mislabelled sequences. Species-level annotations were not considered in Leray et al (2019), and we found incorrectly annotated sequences at all taxonomic levels. As environmental samples contain highly complex DNA signal from various organisms, primer choice is critical for species-level identification (Collins et al, 2019).…”

BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries?

“…The taxonomic reliability of GenBank has often been questioned [e.g. 31], although the actual overall data quality is much better than often assumed [32]. Because BOLD is a workbench for the DNA barcode research community, it will always contain sequences from specimens whose identifications are being refined.…”

How to design optimal eDNA sampling strategies for biomonitoring in river networks

“…Research on molecular and bioinformatic aspects of eDNA analyses has massively expanded within the last few years [Alberdi et al, 2017;Beng and Corlett, 2020;Calderón-Sanou et al, 2019;Deiner et al, 2017;Ficetola et al, 2016;Garlapati et al, 2019;Leray et al, 2019]. Much less focus, however, has been attributed to the "ecology of eDNA", namely "its origin, state, transport, and fate within the environment" [Barnes and Turner, 2015], and how these factors influence its detection [Barnes and Turner, 2015;Harrison et al, 2019].…”