Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia

Leite, Barbara R.; Vieira, Pedro E.; Teixeira, Marcos A. L.; Lobo-Arteaga, Jorge; Hollatz, Cláudia; Borges, Luísa M. S.; Duarte, Sofia Alexandra Ferreira; Troncoso, Jesús Souza; Costa, Filipe O.

doi:10.1016/j.rsma.2020.101307

Cited by 32 publications

(57 citation statements)

References 68 publications

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“…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.…”

Section: Discussionsupporting

confidence: 84%

“…Further, two major results have been emerged. 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.…”

Section: Discussionmentioning

confidence: 87%

“…Working on members of two taxa, the Anthozoa and Hydrozoa of the phylum Cnidaria and the class Ascidiacea of the phylum Chordata, our analyses showed that important reference libraries lack reliable barcodes for these dominant marine macroinvertebrate species. Results further revealed a wide range of di culties and inconsistencies, including taxonomic congruency of the COI barcode records on the one hand and possible cryptic diversity (sensu Leite et al [28]), that should be further studied, on the other hand. The above clearly affect the wholeness of the ERMS list, as only 52.3% and 58.4% of the cnidarians and tunicates, respectively, of the short list of seemingly well 'barcoded species' were noted to have con rmed complete BoLD pages, further lighting that only 11.44% of the tunicate data and 17.07% of the cnidarian data in the ERMS lists are reliable and fully supported (July 2019 state).…”

Section: Discussionmentioning

confidence: 97%

“…Reliable barcode reference libraries are of particular importance [5]. It is evident that the level of taxonomic detection and degree of accuracy is directly contingent on the newly developed molecular-biology depositories, the reference libraries completion and reliability of the DNA records [26][27][28][29]. Given our increased reliance on molecular taxonomy as a robust tool [4], strengthening the existing reference libraries is a necessitate for a wide range of scienti c and applied purposes, such as monitoring, eDNA and metabarcoding approaches, all targeting matched identi cations and the assessments of biodiversity and abundance [5,[14][15][16][17]29] .…”

Section: Discussionmentioning

confidence: 99%

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

Paz

Rinkevich

2020

Preprint

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BackgroundAll-inclusive DNA barcoding libraries in the storage and analysis platform of the BoLD (Barcode of Life Data) system are essential for the study of the marine biodiversity and are pertinent for regulatory purposes, including ecosystem monitoring and assessment, such as in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). Here we investigate knowledge gaps in the lists of DNA barcoded organisms within the Cnidaria (Anthozoa and Hydrozoa) and Ascidiacea reference libraries of the European Register of Marine Species (ERMS) dataset (402 ascidians and 1200 cnidarian species). ERMS records were checked species by species, against publicly available sequence information and the other data stored in BoLD pages. ResultsResults revealed that just 22.9% and 29.2% of the listed ascidians and cnidarians species, respectively, are BoLD’s barcoded species, of which, 58.4% and 52.3% of the seemingly barcoded species, respectively, were noted to have complete BoLD pages. Thus, only 11.44% of the tunicate and 17.07% of the cnidarian data in the ERMS lists are of high quality. Deep analyses revealed seven common types of gaps in the list of the barcoded species in addition to a wide range of discrepancies and misidentifications, discordances and errors primarily in the GenBank mined data as with the BINs assignments, and more. ConclusionsGap knowledge in barcoding of important taxonomic marine groups exist and in addition, quality management elements (quality assurance and quality control) were not employed when using the list for national monitoring projects, for regulatory compliance purposes and other purposes. Even though Bold is the most trustable DNA barcoding reference library, worldwide projects of DNA barcoding are needed in order to close these gaps of mistakes, verifications, missing data and unreliable sequences labs. Tight quality control and quality assurance is important to close the knowledge gaps of Barcoding of the European recommended ERMS reference library.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

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

Paz

Rinkevich

2020

Preprint

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“…Although completing the gaps in reference libraries is essential, careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications (Couton et al 2019, Weigand et al 2019, Leite et al 2020. To this end, taxonomic expertise remains crucial for an accurate identification of the specimens used to originate the reference sequences.…”

Section: Incompleteness Of Reference Sequences Databases For Nismentioning

confidence: 99%

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Duarte

Vieira

Lavrador

et al. 2020

Preprint

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17In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to 18 biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic 19 review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, 20 through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental 21 DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. 22 2 seeking the best approach for detecting the broadest range of species, while minimizing the 38 chances of false positives and false negatives detection. 39 40 Keywords: Marine and coastal ecosystems; non-indigenous species; biosurveillance; (e)DNA 41 metabarcoding 42 43

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General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

et al. 2022

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Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTU) approach of our raw reads and assigned it taxonomically (i) in combination with publicly available reference sequences (open databases) or (ii) with an OSU (Operational Sequence Units) database approach, using a curated database of reference sequences generated from specimen barcoding (closed database). We show both approaches gave comparable results for common species. However, the commonalities between the approaches decreased with read abundance and were thus less reliable and not comparable for rare species. The success of the zOTU approach depended on the suitability, rather than the size, of a reference database.Contrastingly, the OSU approach used reliable DNA sequences and thus often enabled species-level identifications, yet this resolution decreased with the recent phylogenetic age of the species. We show the need to include target group coverage, outgroups and full taxonomic annotation in reference databases to avoid misleading annotations that can occur when using short amplicon sizes as commonly used in eDNA metabarcoding studies. Finally, we make general suggestions to improve the construction and use of reference databases for metabarcoding studies in the future.

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Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia

Cited by 32 publications

References 68 publications

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

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

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

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