Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution

Abstract

Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North‐East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%–32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution.

Compatibility of Diatom Valve Records With Sedimentary Ancient DNA Amplicon Data: A Case Study in a Brackish, Alkaline Tibetan Lake

“…Currently, there are no reference rbcL sequences for Cavinula; thus, none of the ASVs could be annotated to the latter genus, whereas many ASVs corresponded to Navicula sp. Therefore, it is possible that some ASVs assigned to Navicula correspond to Cavinula in the valve data set, because the use of synonyms (and misidentified taxa) is not uncommon in the public databases (Fort et al, 2021). Despite the gaps in the reference databases, the sedaDNA data set contained a much higher diversity of diatoms.…”

Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank

“…Public databases are increasingly being used in multifarious ways by researchers from various biological fields ( Duck et al, 2016 ). Researchers have raised concerns about the use of misidentified sequences in succeeding studies ( Stavrou et al, 2018 ; Fort et al, 2021 ). A substantial number of Xylodon ITS and nrLSU sequences were misidentified or not updated in taxonomy in GenBank ( Tables S1 and S2 ).…”

Marine-Sulfated Polysaccharides Extracts Exhibit Contrasted Time-Dependent Immunomodulatory and Antiviral Properties on Porcine Monocytes and Alveolar Macrophages

“…were collected on the beach at Plestin les Grèves (Brittany, France) and the biomass of the bulk samples analyzed contained a mixture of two foliose Ulva species, predominantly U. lacinulata Kützing (previously known as U. laetevirens Areshoug or U. armoricana Dion, Reviers & Coat [ 26 ]), and a lower amount of Ulva sp. A (previously known as U. rigida [ 27 ]). Algae were molecularly characterized by Pristine coasts company.…”