The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Diversity, Journal Year: 2022, Volume and Issue: 14(3), P. 213 - 213

Published: March 13, 2022

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid effective tool for species identification. The growth barcodes as resource biologists followed advances in computational sequencing technology that have enabled high-throughput applications. global barcode database is expanding to represent diversity on Earth thanks efforts international consortia biological collections. Today, instrumental advancing our understanding how evolve, they interact, we can slow down their extirpation extinction. This review focuses current applications sequences address fundamental lines research, well new which will play central role.

Language: Английский

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COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(4), P. 933 - 945

Published: Jan. 19, 2023

Reference databases with wide taxonomic coverage are greatly needed in many fields of biology, most particularly for the assignment metabarcoding sequences. Therefore, it is fundamental to be able access and pool data from different primary databases. The COInr database a freely available, easy-to-access COI reference sequences extracted BOLD NCBI nucleotide It comprehensive database: not limited taxon, gene region or rank; therefore, good starting point creating custom Sequences dereplicated between within taxa. Each taxon has unique identifier (taxID), avoid ambiguous associations homonyms synonyms source database. TaxIDs form coherent hierarchical system fully compatible taxIDs, allowing their full ranked lineages created. mkcoinr tool series Perl scripts designed download NCBI, build customize according users' needs. possible select eliminate list taxa, specific region, minimum resolution, add new sequences, format blast, vtam, qiime rdp classifier. This semi-automated pipeline using command lines Linux environment. can downloaded https://doi.org/10.5281/zenodo.6555985 its documentation available at https://github.com/meglecz/mkCOInr.

Language: Английский

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Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

Water, Journal Year: 2021, Volume and Issue: 13(3), P. 331 - 331

Published: Jan. 29, 2021

Benthic macroinvertebrates are among the most used biological quality elements for assessing condition of all types aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review 90 publications on use DNA metabarcoding benthic in bioassessments. Metabarcoding bulk macrozoobenthos has been preferentially waters, whereas marine environmental (eDNA) from sediment communities deployed artificial structures favored. extraction done predominantly through commercial kits, cytochrome c oxidase subunit I (COI) been, far, marker, occasionally combined with others, namely, 18S rRNA gene. include lack standardized protocols broad-coverage primers, incompleteness reference libraries, inability to reliably extrapolate abundance data. In addition, morphology versus benchmarking ecological status biotic indexes required allow general implementation higher end-user confidence. The increased sensitivity, high throughput, faster execution can provide much spatial temporal data resolution status, thereby being more responsive immediate management needs.

Language: Английский

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Meta‐Fish‐Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes

Journal of Fish Biology, Journal Year: 2021, Volume and Issue: 99(4), P. 1446 - 1454

Published: July 16, 2021

Abstract The accuracy and reliability of DNA metabarcoding analyses depend on the breadth quality reference libraries that underpin them. However, there are limited options available to obtain curate huge volumes sequence data public repositories such as NCBI BOLD. Here, we provide a pipeline download, clean annotate mitochondrial for given list fish species. Features this include (a) support multiple metabarcode markers; (b) searches species synonyms taxonomic name validation; (c) phylogeny assisted control identification removal misannotated sequences; (d) automatically generated coverage reports each new GenBank release update; (e) citable, versioned DOIs. As an example ready‐to‐use curated library marine freshwater fishes U.K. To augment environmental specifically, 241 MiFish‐12S sequences 88 species, make primer sets useful sequencing these. This brings common fragment 93%, opening avenues scaling up across wide spatial gradients. Meta‐Fish‐Lib is hosted at https://github.com/genner-lab/meta-fish-lib .

Language: Английский

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The Future of DNA Barcoding: Reflections from Early Career Researchers

Diversity, Journal Year: 2021, Volume and Issue: 13(7), P. 313 - 313

Published: July 9, 2021

Over the last two decades, use of DNA barcodes has transformed our ability to identify and assess life on planet. Both strengths weaknesses method have been exemplified through thousands peer-reviewed scientific articles. Given novel sequencing approaches, currently capable generating millions reads at low cost, we reflect questions: What will future bring for barcoding? Will identification species using short, standardized fragments stand test time? We present reflected opinions early career biodiversity researchers in form a SWOT analysis discuss answers these questions.

Language: Английский

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Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 848, P. 157617 - 157617

Published: July 25, 2022

Ecological restoration of terrestrial environments is a globally important process to combat the loss biodiversity and ecosystem services. Holistic monitoring restored biota active management necessary improve processes outcomes, provide evidence stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding used as tool because it able generate data rapidly, accurately, non-destructively, reliably, on wide breadth organisms from soil microbes mammals. The overall objective this review discuss key factors consider in use for ecosystems, hopefully improving monitoring, ultimately, outcomes. We identified majority eDNA based studies currently conducted Europe, North America, Australia, almost half total were published 2021-22. Soil was most popular sample substrate, microbial communities targeted taxa, forests studied ecosystem. suggest there no 'one size fits all' approach using eDNA, survey design. Factors include substrate selection, collection storage, assay interpretation, all which require careful planning obtain reliable, accurate information can be decision making. explore future directions research argue useful 'toolkit', but requires informed application greater accessibility by spectrum stakeholders.

Language: Английский

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DROP: Molecular voucher database for identification of Drosophila parasitoids

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(7), P. 2437 - 2454

Published: June 4, 2021

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due lack sequenced voucher specimens by experts. Sometimes a large number sequences are available, but with too errors allow identification. Here, we address this problem for parasitoids Drosophila introducing curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying challenging poses major impediment realize the full potential model system in studies ranging from mechanisms food webs, biological control suzukii. In DROP, genetic data linked and, where possible, taxonomists vetted through direct comparison primary type material. To initiate 154 strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, six proteomes drawn total 183 operational taxonomic units (OTUs): 114 described parasitoid species 69 provisional species. We found richness heavily underestimated provide an updated catalogue community. offers accurate improves cross-referencing between individual that hope will catalyse research on diverse fascinating system. Our effort should also serve example researchers facing similar problems other organisms.

Language: Английский

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Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions

Diversity, Journal Year: 2023, Volume and Issue: 15(2), P. 174 - 174

Published: Jan. 26, 2023

The introduction of non-indigenous species (NIS) is one the major threats to integrity European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, accuracy taxonomic assignments largely dependent on completion and reliability DNA barcode reference libraries. As such, we aimed compile audit a library marine invertebrate NIS occurring in Europe. To do so, compiled list using three databases: Alien Species Information Network (EASIN), System Aquatic Non-indigenous Cryptogenic (AquaNIS), World Register Introduced Marine (WRiMS). For each species, retrieved available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from Barcode Life Data (BOLD) used Barcode, Audit & Grade (BAGS) check congruence between morphospecies names Index Numbers (BINs). From 1249 compiled, approximately 42% had records BOLD, among which 56% were discordant. We further analyzed these cases determine causes discordances attributed additional annotation tags. Of 622 discordant BINs, after revision, 35% successfully solved, increased number detected metabarcoding datasets 12 16. fair BINs remained Reliability particularly critical case NIS, where erroneous identification may trigger action or inaction when not required.

Language: Английский

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Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: March 28, 2024

Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of terrestrial aquatic habitats world. DNA barcoding metabarcoding are now widely used in both research routine practices involving mosquitoes. However, these methodologies rely on information available databases consisting barcode sequences representing taxonomically identified voucher specimens. In this study, we assess availability public data for mosquitoes online databases, focusing specifically two most markers Culicidae: COI ITS2. addition, test hypotheses possible factors affecting species coverage (i.e., percentage covered databases) different countries occurrence gap COI. Our findings showed differences publicly repositories, with a taxonomic or 28.4-30.11% BOLD + GenBank, 12.32% ITS2 GenBank. Afrotropical, Australian Oriental biogeographic regions had lowest coverages, while Nearctic, Palearctic Oceanian highest. The Neotropical region an intermediate coverage. general, higher diversity numbers medically important lower Moreover, number endemic tended to have Although our analyses suggested that boundaries need be revised half mosquito additional must gathered confirm results allow explaining gap. We hope study can help guide regional inventories completion reference library barcodes all species.

Language: Английский

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On the Diversity of Phyllodocida (Annelida: Errantia), with a Focus on Glyceridae, Goniadidae, Nephtyidae, Polynoidae, Sphaerodoridae, Syllidae, and the Holoplanktonic Families

Diversity, Journal Year: 2021, Volume and Issue: 13(3), P. 131 - 131

Published: March 17, 2021

Phyllodocida is a clade of errantiate annelids characterized by having ventral sensory palps, anterior enlarged cirri, axial muscular proboscis, compound chaetae (if present) with single ligament, and lacking dorsolateral folds. Members most families date back to the Carboniferous, although earliest fossil was dated from Devonian. holds 27 well-established morphologically homogenous clades ranked as families, gathering more than 4600 currently accepted nominal species. Among them, Syllidae Polynoidae are specious polychaete groups. Species mainly found in marine benthos, few inhabit freshwater, terrestrial planktonic environments, occur intertidal deep waters all oceans. In this review, we (1) explore current knowledge on species diversity trends (based traditional concept molecular data), phylogeny, ecology, geographic distribution for whole group, (2) try identify main gaps, (3) focus selected families: Alciopidae, Goniadidae, Glyceridae, Iospilidae, Lopadorrhynchidae, Polynoidae, Pontodoridae, Nephtyidae, Sphaerodoridae, Syllidae, Tomopteridae, Typhloscolecidae, Yndolaciidae. The highest richness concentrated European, North American, Australian continental shelves (reflecting strong sampling bias). While data come shallow coastal surface environments world oceans clearly under-studied. overall indicate that new descriptions constantly added through time less 10% known have barcode information available.

Language: Английский

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