Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(4), P. 742 - 755

Published: Dec. 8, 2022

Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, sciences and monitoring. Thereby, the taxonomic identification species their sequences relies strongly on reference databases that link genetic to names. These vary completeness availability, depending group studied region targeted. The incompleteness an important argument explain nondetection by supposedly present. However, there exist further generally overlooked problems with can lead false inaccurate inferences assignment. Here, we synthesize all possible inherent databases. In particular, identify a complete, mutually nonexclusive list seven classes challenges when it comes selecting, developing database for are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) (v) low resolution, (vi) missing taxa (vii) intraspecific variants. For each problem identified, provide description consequences assignment process. We illustrate respective examples taken literature obtained quantitative analyses public databases, GenBank BOLD. Finally, discuss solutions identified how navigate them. Only raising users' awareness limitations data will adequate interpretations these be achieved.

Language: Английский

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Environmental DNA as an emerging tool in botanical research

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(2)

Published: Jan. 12, 2023

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species communities), means of elucidating biological interaction networks, window into understanding patterns biodiversity. However, only recently potential eDNA realized in botanical world. Here we synthesize state applications systems with emphases on aquatic, ancient, contemporary sediment, airborne systems, focusing both single-species approaches multispecies community metabarcoding. Further, describe how abiotic biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, relative abundance influence utilization interpretation results. Lastly, explore several areas opportunities for further development tools plants, advancing our knowledge efficacy, utility, cost-effectiveness, ultimately facilitating increased adoption analyses systems.

Language: Английский

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Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by DNA metabarcoding

Journal of Applied Ecology, Journal Year: 2022, Volume and Issue: 59(6), P. 1484 - 1495

Published: Feb. 24, 2022

Abstract Gardens are important habitats for pollinators, providing floral resources and nesting sites. There high levels of public support growing ‘pollinator‐friendly’ plants but while plant recommendation lists available, they usually inconsistent, poorly supported by scientific research target a narrow group pollinators. In order to supply the most appropriate resources, there is clear need understand foraging preferences, range across season within horticultural landscapes. Using an innovative DNA metabarcoding approach, we investigated preferences four groups pollinators in large diverse, agricultural landscape, flowering over 2 years, significantly improving on spatial temporal scale that can be achieved using observational studies. Bumblebees, honeybees, non‐corbiculate bees hoverflies visited 191 taxa. Overall were shared between different types significant differences seen used abundantly (Hymenoptera) (Diptera). Floral resource use strongly associated with seasonal changes plants, relying dominant found each season, consistent both years. The identified categorised according their native status investigate value non‐native plants. majority near‐native origin, proportion naturalised increased during late summer autumn. Synthesis applications . Plant should distinguish provide evidence‐based recommendations throughout year include as well United Kingdom Northern Europe. Specific management reducing mowing encourage such dandelion Taraxacum officinale buttercups Ranunculus spp., scrub bramble Rubus fruticosus

Language: Английский

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Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(23), P. 6345 - 6362

Published: Sept. 10, 2022

Abstract Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, ultimately leading species declines. To understand mechanisms behind community shifts declines, as well monitoring managing impacts, a effort must be made characterize plant–pollinator detail, across different habitat types, latitudes, elevations, levels types disturbances. Generating data this scale will only feasible with rapid, high‐throughput methods. Pollen DNA metabarcoding provides advantages throughput, efficiency taxonomic resolution over traditional methods, such microscopic pollen identification visual observation interactions. This makes it ideal for understanding complex ecological networks responses change. is currently being applied assess interactions, survey ecosystem change model spatiotemporal distribution allergenic pollen. Where samples available from past collections, has been used compare contemporary ecosystems. New avenues research possible expansion intraspecific identification, analysis ancient samples, increased use museum herbarium specimens. Ongoing developments sequencing technologies can accelerate progress towards these goals. Global happening rapidly, we anticipate that methods critical evolutionary processes support biodiversity, predicting responding impacts

Language: Английский

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Using DNA Metabarcoding to Identify Floral Visitation by Pollinators

Diversity, Journal Year: 2022, Volume and Issue: 14(4), P. 236 - 236

Published: March 24, 2022

The identification of floral visitation by pollinators provides an opportunity to improve our understanding the fine-scale ecological interactions between plants and pollinators, contributing biodiversity conservation promoting ecosystem health. In this review, we outline various methods which can be used identify visitation, including plant-focused insect-focused methods. We reviewed literature covering ways in DNA metabarcoding has been answer questions relating plant use discuss findings research. present detailed methodological considerations for each step workflow, from sampling through amplification, finally bioinformatic analysis. Detailed guidance is provided researchers utilisation these techniques, emphasising importance standardisation improving reliability results. Future opportunities directions using molecular analyse plant–pollinator are then discussed.

Language: Английский

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Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Jan. 25, 2024

Abstract One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an reference sequence dataset marker choice. Therefore, developing such a has been long-term ambition, especially Viridiplantae kingdom. Typically, datasets are constructed with sequences downloaded from general public databases, which can carry and other relevant errors. Herein, we curated (i) global dataset, (ii) European crop (iii) 27 EU countries ITS2 barcoding vascular plants. To that end, first developed pipeline script entails automated curation stage comprising five filters, manual correction misclassified taxa, addition newly sequenced species. The allows easy updating datasets. With this approach, 13% sequences, corresponding 7% species originally imported GenBank, were discarded. Further, 259 manually added now comprises 307,977 111,382 plant

Language: Английский

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Pollen metabarcoding reveals a broad diversity of plant sources available to farmland flower visitors near tropical montane forest

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 7, 2025

Despite the widely recognized role of pollinators in ecosystem services, we currently have a poor understanding contribution Natural Protected Areas neighboring agricultural landscapes to crop pollinator diversity and plant-pollinator interactions. Here, conducted monthly surveys over period one year study insect visitors dominant fruit crops-avocado, plum, apple, blackberry-and used pollen DNA metabarcoding characterize community plant sources around low-intensive farmland bordered by protected montane forest Costa Rica. We found that crops native plants had distinct communities flower visitors, suggesting presence fine-scale habitat differences. coupled with custom-built reference database, enabled us identify among samples high taxonomic resolution (species or genus level). carried from large taxa, including species forests highland páramos The composition were variable across groups. Wildflower such as bumblebees syrphid flies, use diverse range taxa at similar levels managed honeybees. This indicates potential pollination services flora. Overall, our suggests farming practices promote common ruderals combined nearby contribute maintaining provide crucial services.

Language: Английский

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Unveiling Heterospecific Pollen Deposition in Ranunculus Plants Along a Land‐Use Gradient Through DNA Metabarcoding

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: March 27, 2025

ABSTRACT Animal pollination, the transfer of pollen by animal agents, is essential for plant reproduction. Methods like microscopy and DNA metabarcoding have been used to investigate transport plant–pollinator interactions. metabarcoding, in particular, a reliable method identify origins mixed samples. Although it has mainly study pollinators' dietary patterns, does not provide insights from plant's perspective, such as type viable received. We aimed explore potential analyse heterospecific plants semi‐natural agricultural landscapes along land‐use intensity gradient. collected stigmas three closely related Ranunculus species ( R. acris , bulbosus repens ) 20 grassland plots Germany with varying intensities flowering diversity subjected them internal transcribed spacer 2 (ITS2) metabarcoding. Our results revealed nonlinear relationship between richness on stigmas. The lowest occurred intermediate richness, whereas low or high showed greater diversity. Reduced found mostly LUI plots, forces pollinators visit multiple thus increases transfer. Plots contrary, likely balanced mix resources pollinators, visiting within foraging round decreasing amount pollen. Increased at high‐richness may result competition pollinator‐rich communities. show that powerful tool assessing diversity, revealing heavily influenced community composition. This approach provides novel into pollinator fidelity pollination outcomes across diverse environments.

Language: Английский

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A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture‐Based DNA Metabarcoding

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT Pollen identification (ID) and quantification is important in many fields, including pollination ecology agricultural sciences, efforts to explore optimal molecular methods for identifying low concentrations of DNA from plant mixtures are increasing, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy time‐consuming, requires expertise has limited accuracy throughput. Molecular barcoding approaches being explored offer improved The common approach, amplicon sequencing, employs PCR amplification isolate barcodes, introduces significant bias, impairing downstream quantification. We apply a novel hybrid capture approach artificial improve upon current taxon methods. method randomly fragments uses RNA baits which allows duplicate removal, reducing bias. Four reference databases were used A restricted matK database containing only species yielded sequence highly correlated with input proportions, demonstrating the potential usefulness metabarcoding mixtures. Identification power was further tested two libraries constructed publicly available sequences: plastid barcode RefSeq complete chloroplast references. Single barcode‐based did not consistently resolve or genus level. performed better qualitatively had coverage (relative here) introduced issues. At family level, both comparable qualitative results, quantitatively. Whilst developed here tremendous potential, choice expansion one most factors allowing quantitative full set genomic regions screened by this method.

Language: Английский

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Pollen DNA metabarcoding reveals cryptic diversity and high spatial turnover in alpine plant–pollinator networks

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(23), P. 6377 - 6393

Published: Sept. 6, 2022

Alpine plant-pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding how environmental factors and spatiotemporal variability shape these communities. Here, investigate what drives structure beta diversity metacommunity from Australian region using two approaches: pollen DNA metabarcoding (MB) observations. Individual pollinators often carry multiple plant species, therefore expected MB to reveal more diverse complex network structure. We used gene regions (ITS2 trnL) identify species present loads 154 insect pollinator specimens three habitats construct networks, compared them networks based on observations alone. interaction turnover across space for both types evaluated their differences phylogenetic diversity. found significant structural between networks; notably, were much less specialized but than observation with detecting many cryptic species. Both approaches revealed that pollination very generalized, estimated high spatial (0.79) rewiring (0.6) as well (0.68) driven habitat larger interactions detected MB. Overall, our findings show microclimatic heterogeneity fine-scale networks.

Language: Английский

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