Benchmarking the discrimination power of commonly used markers and amplicons in marine fish (e)DNA (meta)barcoding

Published: June 3, 2024

Environmental DNA (eDNA) metabarcoding is revolutionizing the study of aquatic ecosystems, enabling high-throughput analysis biodiversity with minimal disturbance. Despite its potential to support fisheries management, species identification and downstream reliability are hindered by lack standardization in fragment choice. This compares discrimination power three markers used marine fish eDNA —12S rRNA, 16S cytochrome oxidase subunit I (COI)— as well two amplicons for each. We analyzed sequences from NCBI GenBank 10 orders Actinopterygii, including mitochondrial genomes. assessed determining percentage monophyletic Neighbor-Joining trees calculating average congeneric divergences data sets: one genomic regions extracted genomes (771 species) another independent each region (3879 species). Among (meta)barcoding amplicons, genomes’ dataset, Folmer Leray-Lobo had highest discriminatory power, 89.2% 87% species, respectively, while 12S Teleo lowest at 71.6%. Conversely, using sequences, percentages 64.8% 63.5%, Ac16S 83.0%. Species influenced marker’s substitution rate, length, target order, quality reference sequence data. recommend considering differences amplicon selection, especially species-level identifications. advise a standard multi-marker approach under certain scenarios, namely when presence close expected.

Language: Английский

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Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions

Ecological Indicators, Journal Year: 2022, Volume and Issue: 145, P. 109603 - 109603

Published: Nov. 1, 2022

Freshwater systems are experiencing rapid biodiversity losses resulting from high rates of habitat degradation. Ecological condition is typically determined through identifying either macroinvertebrate or diatom bioindicator assemblages and comparing them to their known tolerance stressors. These comparisons conducted at family genus levels depending on the availability taxonomic keys expertise for focal groups. The objective this study was test whether a more taxonomically comprehensive assessment communities in benthic samples can provide different perspective ecological conditions. DNA metabarcoding used identify macroinvertebrates diatoms kick-net collected sites with status. Sites 'good' were associated higher beta diversity as well slightly directed connectance modularity indicating resilience compared 'fair' sites. Indicator value correlation analyses data detect 29 site indicator species consistent bioindicators expected relative tolerances. trophic network analysis also recovered 11 keystone taxa. This demonstrates importance breadth across generating biotic ecosystem status, potential scale-up assessments freshwater condition, stability, resilience.

Language: Английский

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Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(23), P. 6130 - 6146

Published: Oct. 5, 2022

Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies mitochondrial genes, other artefacts lead taxonomic inflation, which compromise reliability biodiversity inventories. Here, we explore potential bioinformatic approach jointly "denoise" filter nonauthentic sequences from metabarcode reads obtain reliable soil beetle inventories address open questions in research, such as scale dispersal constraints different layers. We sampled cloud forest communities 49 sites Anaga peninsula Tenerife (Canary Islands). performed whole organism community DNA (wocDNA) metabarcoding, built local reference database with COI barcode 310 Coleoptera for filtering identification metabarcoded species. This resulted haplotype data after considerably reducing artefacts. Comparing our results previous inventories, found: (i) new records, potentially representing undescribed species; (ii) (iii) validated phylogeographic structure when compared traditional sequencing approaches. Analyses also revealed evidence higher constraint within deeper communities, closer surface. The combined power barcoding metabarcoding contribute mitigate important shortfalls associated diversity data, thus unresolved vast fraction.

Language: Английский

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Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at within-species level. Through analysis eDNA samples collected from Peter Great Gulf Japan Sea, this study, we aimed evaluate identification Amplicon Sequence Variants (ASVs) marine among abundant species

Language: Английский

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Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(8)

Published: Aug. 1, 2024

Abstract Rivers are crucial ecosystems supporting biodiversity and human well‐being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms taxonomic resolution scalability. This study explores the application DNA metabarcoding analysis both bulk environmental (eDNA) samples for comprehensive assessment macrozoobenthic biodiversity, detection invasive endangered species, evaluation ecological status northwestern Spain. homogenized water eDNA revealed a mean 100 87 macrozoobenthos species per sample respectively. However, specific composition was significantly different with only 27.3% total being shared. It not possible to identify all OTUs level; 17.43% 49.4% generated could be identified level samples, Additionally, 11 exotic (two first records Iberian Peninsula another three Asturias region) one were detected by molecular tools. Molecular showed significant correlations EQR values (Ecological Quality Ratio) IBMWP index, differences inferred noted, tending indicate higher status. Overall, offers promising approach biomonitoring, providing insights into within single analysis. Further optimization intercalibration required its implementation routine programmes, but scalability multi‐tasking capabilities position it as valuable tool integrated monitoring ecosystems.

Language: Английский

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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(4), P. 2244 - 2244

Published: Feb. 17, 2022

Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized genetics research including population studies. However, the reconstruction of mitogenome is complicated by nuclear DNA (mtDNA) segments (NUMTs) co-align with mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% 10%, were assessed ability to produce from previously generated WGS dataset. Variants associated NUMTs detected in alignments 91 917 (~8%) Swedish samples when frequency threshold was applied. The 413 observed NUMT variants predominantly two regions (nps 12,612–13,105 16,390–16,527), which consistent documented NUMTs. number reduced ~97% (400) using 10% threshold. Furthermore, inconsistent platinum-quality dataset respect These analyses illustrate may necessary ensure generation reliable resources.

Language: Английский

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MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: July 15, 2020

Abstract Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes fungi animals such as for molecular ecology and biomonitoring applications in sectors academic research regulatory agencies industry. Current popular bioinformatic pipelines support microbial fungal marker analysis, while ad hoc methods are often process animal metabarcode markers the same study. MetaWorks provides a harmonized processing environment, pipeline, taxonomic assignment approach demultiplexed Illumina reads all biota using wide range 16S, ITS, COI. A Conda environment provided quickly gather most programs dependencies pipeline. Several workflows as: taxonomically assigning exact sequence variants, an option operational units, facilitates single-read processing. Pipelines automated Snakemake minimize user intervention facilitate scalability. All use RDP classifier provide assignments with confidence measures. We extend functionality 16S (bacteria), ITS (fungi), 28S also COI (animals), rbcL (eukaryotes, land plants, diatoms), 12S (fish), 18S diatoms) (fungi, plants). properly handles by trimming flanking conserved rRNA gene regions well protein coding genes providing two options removing obvious pseudogenes. available at https://github.com/terrimporter/MetaWorks along quick-start instructions test data, detailed workflow descriptions, tutorial new users.

Language: Английский

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Nuclear mitochondrial DNA sequences in the rabbit genome

Mitochondrion, Journal Year: 2022, Volume and Issue: 66, P. 1 - 6

Published: July 13, 2022

Numtogenesis is observable in the mammalian genomes resulting integration of mitochondrial segments into nuclear (numts). To identify numts rabbit, we aligned and genomes. Alignment significance threshold was calculated individual characteristics were analysed. We found 153 genome. The GC content significantly lower than their genomic flanking regions or genome itself. frequency three mammalian-wide interspersed repeats increased proximity numts. decreased around strengthen theory which supposes a link between DNA structural instability numt integration.

Language: Английский

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Bioinformatics and Its Application in Computing Biological Data

Published: Jan. 1, 2022

Bioinformatics has become an important part of a variety biological fields. methods such as signal processing and image enable the extraction conclusions that are useful from larger amounts raw data in experimental molecular biology. In realm genetics, it aids annotation sequencing genomes well their reported mutations. Through literature, text mining, creation gene ontologies biological, organisation querying data. It can also be used to find expression control proteins genes. tools help analysis, comparison, interpretation genomic genetic data, knowing evolutionary elements investigation cataloguing pathways networks on more integrated level, which crucial aspects systems Structural biology modelling simulation RNA, proteins, DNA, biomolecular interactions.

Language: Английский

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Network structure and taxonomic composition of tritrophic communities of Fagaceae, cynipid gallwasps and parasitoids in Sichuan, China

Insect Conservation and Diversity, Journal Year: 2024, Volume and Issue: 17(6), P. 1046 - 1071

Published: July 16, 2024

Abstract A key question in insect community ecology is whether parasitoid assemblages are structured by the food plants of their herbivore hosts. Tritrophic communities centred on oak‐feeding cynipid gallwasps one best‐studied tritrophic communities. Previous work suggests that host plant identity a much stronger predictor oak–cynipid interactions than cynipid–parasitoid interactions. However, these relationships have not been formally quantified. We reason potential for ‘bottom‐up’ effects should increase with phylogenetic diversity. We, therefore, generated quantified interaction network data previously unstudied Sichuan, China, where, addition to Quercus , include Castanea Castanopsis and Lithocarpus . characterise taxonomically compare extent which taxonomy predicts plant–herbivore plant–parasitoid associations. sampled 42,620 galls 176 morphotypes from 23 species, yielding over 4500 specimens 64 morphospecies. Many parasitoids were identifiable chalcidoid taxa present other Holarctic oak communities, Cynipencyrtus (Cynipencyrtidae). As elsewhere, Sichuan dominated generalists. Gallwasp–plant networks significantly more modular parasitoid–plant association networks. Gallwasps specialised (i.e. had higher mean d' values) parasitoids. Parasitoid nevertheless showed significant plant‐associated beta diversity, dominant turnover component. summarise parallels between our study Fagaceae‐associated discuss findings light processes thought structure endophytic herbivores.

Language: Английский

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