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

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

Background 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 a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely ach...

Descrizione completa

Dettagli Bibliografici
Autori principali:	Francesco Mugnai, Federica Costantini, Anne Chenuil, Michèle Leduc, José Miguel Gutiérrez Ortega, Emese Meglécz
Natura:	Articolo
Lingua:	English
Pubblicazione:	PeerJ Inc. 2023-01-01
Serie:	PeerJ
Soggetti:	Reference databases Metabarcoding COI Taxonomic assignment Marine taxa COInr
Accesso online:	https://peerj.com/articles/14616.pdf

Documenti analoghi

How reliable is metabarcoding for pollen identification? An evaluation of different taxonomic assignment strategies by cross-validation
di: Gilles San Martin, et al.
Pubblicazione: (2024-01-01)

To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
di: Adrià Antich, et al.
Pubblicazione: (2021-04-01)

An improved statistical model for taxonomic assignment of metagenomics
di: Yujing Yao, et al.
Pubblicazione: (2018-10-01)

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities
di: Janina Schenk, et al.
Pubblicazione: (2020-03-01)

Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
di: Bachir Balech, et al.
Pubblicazione: (2018-06-01)

A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification
di: Michael Kerr, et al.
Pubblicazione: (2023-07-01)

Short COI markers for freshwater macroinvertebrate metabarcoding
di: Ecaterina Vamos, et al.
Pubblicazione: (2017-09-01)

Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality
di: Xin‐Yi Chua, et al.
Pubblicazione: (2024-11-01)

Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community
di: Molly A. Timmers, et al.
Pubblicazione: (2022-01-01)

Metabarcoding of marine nematodes – evaluation of similarity scores used in alignment-based taxonomy assignment approach
di: Oleksandr Holovachov
Pubblicazione: (2016-11-01)

Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf
di: Mya Breitbart, et al.
Pubblicazione: (2023-03-01)

Metabarcoding of marine nematodes – evaluation of reference datasets used in tree-based taxonomy assignment approach
di: Oleksandr Holovachov
Pubblicazione: (2016-09-01)

COI Metabarcoding Provides Insights into the Highly Diverse Diet of a Generalist Salamander, <i>Salamandra salamandra</i> (Caudata: Salamandridae)
di: Adam J. D. Marques, et al.
Pubblicazione: (2022-01-01)

Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
di: Gemma Henderson, et al.
Pubblicazione: (2019-03-01)

ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
di: Dylan Catlett, et al.
Pubblicazione: (2021-07-01)

Applicability and perspectives for DNA barcoding of soil invertebrates
di: Jéhan Le Cadre, et al.
Pubblicazione: (2024-07-01)

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms
di: Sten Anslan, et al.
Pubblicazione: (2021-09-01)

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea
di: Becky Cribdon, et al.
Pubblicazione: (2020-04-01)

Integrative taxonomy approach to detect spatial and temporal variability of the Mediterranean benthic communities through artificial substrate units (ASUs)
di: Francesco Mugnai, et al.
Pubblicazione: (2023-08-01)

Relevance of DNA barcodes for biomonitoring of freshwater animals
di: Manuel Elías-Gutiérrez, et al.
Pubblicazione: (2023-02-01)

An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand
di: Fabian Gösser, et al.
Pubblicazione: (2023-03-01)

Another crack in the Dark Taxa wall: a custom DNA barcoding protocol for the species-rich and common Eurytomidae (Hymenoptera, Chalcidoidea)
di: Samin Jafari, et al.
Pubblicazione: (2023-05-01)

Optimizing eDNA Metabarcoding Techniques for Assessing Arthropod Communities in Tree‐Related Microhabitats
di: Mohammad Jamil Shuvo, et al.
Pubblicazione: (2025-01-01)

A multi-task CNN learning model for taxonomic assignment of human viruses
di: Haoran Ma, et al.
Pubblicazione: (2021-06-01)

DNA Metabarcoding Improves the Taxonomic Resolution of Visually Determined Diet Composition of Beaked Redfish (Sebastes sp.)
di: Sarah Brown‐Vuillemin, et al.
Pubblicazione: (2025-01-01)

Inferring functional diversity from environmental DNA metabarcoding
di: Céline Condachou, et al.
Pubblicazione: (2023-09-01)

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
di: Adithya Murali, et al.
Pubblicazione: (2018-08-01)

Application of Next-Generation Sequencing for the Determination of the Bacterial Community in the Gut Contents of Brackish Copepod Species (<i>Acartia hudsonica</i>, <i>Sinocalanus tenellus</i>, and <i>Pseudodiaptomus inopinus</i>)
di: Yeon-Ji Chae, et al.
Pubblicazione: (2021-02-01)

ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data
di: Clément Plessis, et al.
Pubblicazione: (2023-10-01)

Interlaboratory study to assess the practical utility of OSAC proposed standard 2021-S-0006: Standard for the use of GenBank for taxonomic assignment of wildlife
di: Khushi K. Patel, et al.
Pubblicazione: (2023-12-01)

Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment
di: S. V. Turanov, et al.
Pubblicazione: (2024-07-01)

A closer look at the taxonomic and genetic diversity of endemic South African Marphysa Quatrefages, 1865
di: Jyothi Kara, et al.
Pubblicazione: (2023-12-01)

BLAST-based validation of metagenomic sequence assignments
di: Adam L. Bazinet, et al.
Pubblicazione: (2018-05-01)

Nanopore short‐read sequencing: A quick, cost‐effective and accurate method for DNA metabarcoding
di: Aimee L. van der Reis, et al.
Pubblicazione: (2023-03-01)

Taxonomic Blind Spots: A Limitation of Environmental DNA Metabarcoding‐Based Detection for Canadian Freshwater Fishes
di: Kevin C. Morey, et al.
Pubblicazione: (2024-11-01)

Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems
di: David Singer, et al.
Pubblicazione: (2021-01-01)

Applications and challenges of DNA barcoding and metabarcoding in African fisheries
di: Hosam Elsaied, et al.
Pubblicazione: (2021-03-01)

taxalogue: a toolkit to create comprehensive CO1 reference databases
di: Niklas W. Noll, et al.
Pubblicazione: (2023-12-01)

VTAM: A robust pipeline for validating metabarcoding data using controls
di: Aitor González, et al.
Pubblicazione: (2023-01-01)

Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort
di: Marvin Kaczmarek, et al.
Pubblicazione: (2022-05-01)