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DNA barcodes enable higher taxonomic assignments in the Acari

Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species pr...

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Autores principales: Young, Monica R., deWaard, Jeremy R., Hebert, Paul D. N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342613/
https://www.ncbi.nlm.nih.gov/pubmed/34354125
http://dx.doi.org/10.1038/s41598-021-95147-8
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author Young, Monica R.
deWaard, Jeremy R.
Hebert, Paul D. N.
author_facet Young, Monica R.
deWaard, Jeremy R.
Hebert, Paul D. N.
author_sort Young, Monica R.
collection PubMed
description Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem’s identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID’s capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success.
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spelling pubmed-83426132021-08-10 DNA barcodes enable higher taxonomic assignments in the Acari Young, Monica R. deWaard, Jeremy R. Hebert, Paul D. N. Sci Rep Article Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem’s identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID’s capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success. Nature Publishing Group UK 2021-08-05 /pmc/articles/PMC8342613/ /pubmed/34354125 http://dx.doi.org/10.1038/s41598-021-95147-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Young, Monica R.
deWaard, Jeremy R.
Hebert, Paul D. N.
DNA barcodes enable higher taxonomic assignments in the Acari
title DNA barcodes enable higher taxonomic assignments in the Acari
title_full DNA barcodes enable higher taxonomic assignments in the Acari
title_fullStr DNA barcodes enable higher taxonomic assignments in the Acari
title_full_unstemmed DNA barcodes enable higher taxonomic assignments in the Acari
title_short DNA barcodes enable higher taxonomic assignments in the Acari
title_sort dna barcodes enable higher taxonomic assignments in the acari
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342613/
https://www.ncbi.nlm.nih.gov/pubmed/34354125
http://dx.doi.org/10.1038/s41598-021-95147-8
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