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

Metabarcoding and Metagenomics, Год журнала: 2024, Номер 8

Опубликована: Окт. 4, 2024

Environmental DNA (eDNA) metabarcoding is revolutionising 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 standardisation in fragment choice. This compares discrimination power three markers used marine fish (e)DNA (meta)barcoding – 12S rRNA, 16S rRNA cytochrome oxidase subunit I (COI) as well two amplicons for each. We analysed sequences from NCBI GenBank 10 orders Actinopterygii (ray-finned fishes), including mitochondrial genomes. assessed determining percentage monophyletic Neighbour-Joining trees calculating congeneric divergences datasets: one genomic regions extracted genomes (771 species) another independent each region (3,879 species). Amongst genomes’ dataset, COI Folmer Leray-Lobo had highest discriminatory power, 89.2% 87.0% species, respectively, while Teleo lowest at 71.6%. Conversely, using these amplicons, percentages 64.8% 63.5%, (Ac16S) 83.0%. Species influenced marker’s evolutionary 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, particularly when presence close expected.

Язык: Английский

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VLF: An R package for the analysis of very low frequency variants in DNA sequences

Biodiversity Data Journal, Год журнала: 2023, Номер 11

Опубликована: Янв. 26, 2023

Here, we introduce VLF , an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for analysis errors DNA sequence records. The allows users assess VLFs aligned trimmed protein-coding by automatically calculating nucleotides or acids each position outputting those that occur under a user-specified (default p = 0.001). These results can then be used explore fundamental population genetic phylogeographic patterns, mechanisms processes at microevolutionary level, such as conservation. Our extends earlier work pertaining implementation Microsoft Excel, which was found both computationally slow error prone. We compare our own herein. Results between two implementations are highly consistent large barcode dataset bird species. Differences readily explained manual human inadequate Linnean taxonomy (specifically, species synonymy). is also applied subset avian barcodes extent biological artifacts level Canada goose ( Branta canadensis ), well within fishes forensic regulatory importance. novelty its benefit over previous include high automation, speed, scalability ease-of-use, desirable characteristics will extremely valuable more data rapidly accumulated popular reference databases, BOLD GenBank.

Язык: Английский

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An assessment of South African small mammal barcode sequence libraries: Implications for future carnivore diet analyses by DNA

African Journal of Ecology, Год журнала: 2023, Номер 62(1)

Опубликована: Ноя. 27, 2023

Abstract DNA metabarcoding requires reference libraries that link sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S (16S b (cyt ) and the hypervariable control region (D‐loop) are routinely used in studies measure genetic diversity animal This study aimed review state of for small South African mammals as constitute a large portion medium carnivore diet. Analyses records revealed 193 mammal species Africa, only 141 have available one or more mitochondrial genes examined. Cyt had highest coverage, with 59.1% represented libraries. COI has 33.7%, rRNA 23.8%, D‐loop 17.6%, lowest coverage 15%. supports use multiple when performing scat metabarcoding, particularly wanting determine component Additionally, it emphasises need build comprehensive linking taxonomically identified

Язык: Английский

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Sheaf Cohomology of Rectangular-Matrix Chains to Develop Deep-Machine-Learning Multiple Sequencing

Deleted Journal, Год журнала: 2024, Номер 1(1), С. 55 - 71

Опубликована: Дек. 16, 2024

The sheaf cohomology techniques are newly used to include Morse simplicial complexes in a rectangular-matrix chain, whose singular values compatible with those of square matrix, which can be for multiple sequencing. equivalence the simplices corresponding graph is proven, as well that filtration probability space. new protocol eliminates problem stochastic stability deep Markov models. paradigm implemented develop deep-machine-learning construction models sequencing, starting from profile model, analytically written. Applications found an amino-acid sequencing model. As result, nucleotide-dependence positions on alignments fully modelized. metrics manifolds discussed. instance application Jukes–Cantor model successfully controlled nucleotide-substitution

Язык: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Ноя. 15, 2021

Abstract 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.

Язык: Английский

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