Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e14616 - e14616

Published: Jan. 9, 2023

In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have good coverage avoid unassigned sequences. However, this goal rarely achieved many geographic regions for several groups. On other hand, more not necessarily better, as sequences databases belonging groups out of studied region/environment context might lead false assignments.

Language: Английский

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Biodiversity Monitoring in Mediterranean Marine Protected Areas: Scientific and Methodological Challenges

Diversity, Journal Year: 2022, Volume and Issue: 14(1), P. 43 - 43

Published: Jan. 10, 2022

Biodiversity is a portmanteau word to indicate the variety of life at all levels from genes ecosystems, but it often simplistically equated species richness; ecodiversity has thus been coined address habitat variety. represents core natural capital, and as such needs be quantified followed over time. Marine Protected Areas (MPAs) are major tool for biodiversity conservation sea. Monitoring both diversity in MPAs therefore mandatory must include inventory periodic surveillance activities. In case inventories, ideal would census habitats, while latter goal can within reach, former seems unattainable. Species should commeasured investigation effort, based on mapping. Both inventories may profit suitability spatial modelling. Periodic actions privilege conspicuous priority habitats. Efficient descriptor taxa ecological indices recommended evaluate environmental status. While obvious that activities carried out with regular recurrence, diachronic mapping rarely out. Time series prime importance detect marine ecosystem change even absence direct human impacts.

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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Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing

PeerJ, Journal Year: 2022, Volume and Issue: 10, P. e13790 - e13790

Published: Aug. 5, 2022

DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode biased toward cytochrome oxidase subunit I (COI) frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental (eDNA) has necessitated multiple marker techniques combined with backed by specimens. Reference barcodes have traditionally been generated Sanger sequencing, however sequencing markers costly for large numbers specimens, requires separate PCR reactions, limits resulting sequences targeted regions. High-throughput genome skimming enable assembly complete mitogenomes, contain the most commonly used loci (e.g., COI, 12S, 16S), well nuclear ribosomal repeat regions ITS1&2, 18S). We evaluated feasibility generate references marine fishes assembling mitogenomes repeats. tested across a taxonomically diverse selection 12 fish from collections National Museum Natural History, Smithsonian Institution. two libraries per test impact shearing method (enzymatic mechanical), extraction (kit-based automated), input concentration. produced all non-chondrichthyans (11/12 species) assembled repeats (18S-ITS1-5.8S-ITS2-28S) taxa. quality completeness mitogenome assemblies was not impacted method, Our results reaffirm that an efficient (at scale) cost-effective mitochondrial common simultaneously, great potential scale future projects facilitate completing fishes.

Language: Английский

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Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: Feb. 28, 2023

Abstract Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration this uncharted protist diversity communities relies essentially on studying genetic markers from environment as taxonomic barcodes. Here we report across 6 large scale spatio-temporal planktonic surveys, half barcodes taxonomically unassigned at genus level, preventing a fine ecological understanding for numerous lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear least described group. We have developed computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, order to infer large-scale patterns 100% similarity marker, overcoming limitation assignment. From spatial perspective, identified 2171 clusters, i.e., sequences with similarity, exclusively shared between Tropical/Subtropical Ocean Mediterranean Sea among all orders 25 ubiquitous clusters within studied marine regions. temporal over 3 time-series, highlighted 39 follow rhythmic recurrence best indicators parasite community’s variation. These withhold potential ecosystem change indicators, mirroring their associated host community responses. Our results underline importance structuring through space time, raising questions regarding host-parasite association specificity trophic mode persistent Syndiniales, while providing an innovative framework prioritizing taxa further description.

Language: Английский

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Revisiting ‘A monograph on the Polychaeta of southern Africa’: establishing taxonomic research priorities in southern Africa

African Journal of Marine Science, Journal Year: 2022, Volume and Issue: 44(1), P. 83 - 100

Published: Jan. 2, 2022

Originally published in 1967, John H Day's work 'A monograph on the Polychaeta of southern Africa' is still used widely to identify polychaetes. However, ongoing taxonomic revisions have revealed that several putative cosmopolitan or locally widespread taxa contained are complexes species with discrete distributions, globally and locally. This study therefore aimed develop lists taxa, including unresolved indigenous species, should be prioritised for revision unlock their hidden diversity. A total 609 (56 families 316 genera) were scored according time since description, global local distribution, availability genetic data vouchers, alien status economic importance, then ranked. At least half reported complexes, a quarter wide probably hiding cryptic Accordingly, we estimate approximately 500 polychaete undescribed Africa. The four highest-scoring (Syllidae, Nereididae, Spionidae Eunicidae) comprise 25% 53–85% cosmopolitans, while multiple considered pests, as bait possible aliens. Prioritised genera (e.g. Eunice, Syllis, Nereis, Prionospio, Dipolydora) Pseudonereis variegata) usually members families, but some not Sabella cf. pavonina, Fimbriosthenelais zetlandica, Paleanotus chrysolepis, Gunnarea gaimardi, Capitella capitata). All taxon levels ensure all most need identified. Ways facilitate discussed.

Language: Английский

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Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(4), P. 818 - 832

Published: Jan. 25, 2023

Abstract Biomonitoring surveys make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases identify species. However, mitochondrial reference data are yet incomplete, only a few genes may be available, or suitability existing sequence is suboptimal for species level resolution. Here, we present dedicated and cost‐effective workflow with no DNA amplification generating complete fish mitogenomes purpose strengthening databases. Two different strategies using long fragment Oxford Nanopore technology coupled enrichment were used. One where achieved by preferential isolation mitochondria followed extraction nuclear depletion (“mitoenrichment”). A second approach takes advantage CRISPR Cas9 targeted scission on previously dephosphorylated (“targeted mitosequencing”). The varied between tissue, species, integrity DNA. mitoenrichment method yielded 0.17%–12.33% sequences target mean coverage ranging from 74.9 805‐fold. mitosequencing experiment native 1.83%–55% 38 2123‐fold coverage. produced homopolymeric regions, tandem repeats, gene rearrangements. We demonstrate that deep fragments can low computational resources in manner, opening discovery nonmodel understudied taxa broad range laboratories worldwide.

Language: Английский

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eDNA metabarcoding warms up a hotspot of marine biodiversity: revealing underrepresented taxa in visual surveys and historical records from the Gulf of California

Marine Biodiversity, Journal Year: 2024, Volume and Issue: 54(2)

Published: Feb. 23, 2024

Language: Английский

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A new genus and species of feather duster worm (Annelida, Sabellidae) from shallow hydrocarbon seeps in the Gulf of Mexico

Biodiversity Data Journal, Journal Year: 2025, Volume and Issue: 13

Published: March 18, 2025

Sabellid species are known to have a broad depth distribution and been reported from various deep-sea habitats, including chemosynthetic systems. Despite this presence, only two identified deep water habitats one has species. When examining hydrocarbon seep systems along the Upper Louisiana Slope in Gulf of Mexico, we observed an abundant sabellid new science. The characters for collected specimens did not match any existing genus. description genus presented, supported by external morphology DNA sequence data (cytochrome c oxidase I). Seepicola viridiplumi gen. nov., sp. nov. gregarious, facultative hyper-epibionts within examined methane communities and, seemingly, blend morphological features genera Perkinsiana Pseudopotamilla . Specimens also several distinctive presence pair peristomial chambers between ventral lappets parallel lamellae short, button-like shape radiolar tips. Abundance estimates S. presented.

Language: Английский

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Contrasting the contributions of 12S eDNA metabarcoding, visual surveys and anaesthetic collections to the historical regional diversity of cryptobenthic and conspicuous fish

Journal of Fish Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 19, 2025

Abstract Taxonomic gaps in community biodiversity assessments are now commonly addressed by combining traditional monitoring methods and environmental DNA (eDNA) metabarcoding, widely recognized for having the ability to uncover rare cryptic diversity. However, only a few studies have assessed efficacy of this novel technique detecting cryptobenthic fishes tested limitations incomplete genetic reference availability historically neglected component fish communities. Our goals were (i) compare conspicuous detections 12S eDNA visual surveys anaesthetic collections, (ii) emerging regional diversity patterns against long‐term historical record Gulf California. Despite adding new local references 36 fishes, metabarcoding detected seven taxa. Visual provided similar results, highlighting collections as primary source, with 57 recovered. Conspicuous had an equal highly complementary contribution surveys. When contemporary from all methods, we recovered 43% 16% relative records. The spatial structure differed expectations showing no differences richness nor composition between Northern Central study highlights that their structuring driven distinct factors compared fishes.

Language: Английский

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