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An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)

PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, howeve...

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Autores principales: Bell, Karen L., Loeffler, Virginia M., Brosi, Berry J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Botanical Society of America 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357121/
https://www.ncbi.nlm.nih.gov/pubmed/28337390
http://dx.doi.org/10.3732/apps.1600110
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author Bell, Karen L.
Loeffler, Virginia M.
Brosi, Berry J.
author_facet Bell, Karen L.
Loeffler, Virginia M.
Brosi, Berry J.
author_sort Bell, Karen L.
collection PubMed
description PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms. We used this reference library, along with the existing bioinformatics pipeline and ITS2 reference library, to identify species in an artificial mixture of nine species of pollen. We have made this database publicly available in multiple formats, to allow use with multiple bioinformatics pipelines, now and in the future. RESULTS: Using the rbcL database, in addition to the ITS2 database, we succeeded in making species-level identifications for eight species and a family-level identification of the ninth species. This is an improvement on ITS2 sequence alone. DISCUSSION: The reference library described here will assist with identification of plant species using rbcL. By making another gene region available for standard barcoding, this will increase the resolution and accuracy of identifications.
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spelling pubmed-53571212017-03-23 An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1) Bell, Karen L. Loeffler, Virginia M. Brosi, Berry J. Appl Plant Sci Genomic Resources Note PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms. We used this reference library, along with the existing bioinformatics pipeline and ITS2 reference library, to identify species in an artificial mixture of nine species of pollen. We have made this database publicly available in multiple formats, to allow use with multiple bioinformatics pipelines, now and in the future. RESULTS: Using the rbcL database, in addition to the ITS2 database, we succeeded in making species-level identifications for eight species and a family-level identification of the ninth species. This is an improvement on ITS2 sequence alone. DISCUSSION: The reference library described here will assist with identification of plant species using rbcL. By making another gene region available for standard barcoding, this will increase the resolution and accuracy of identifications. Botanical Society of America 2017-03-10 /pmc/articles/PMC5357121/ /pubmed/28337390 http://dx.doi.org/10.3732/apps.1600110 Text en © 2017 Bell et al. Published by the Botanical Society of America https://creativecommons.org/licenses/by-nc-sa/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (CC-BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/) ), which permits unrestricted noncommercial use and redistribution provided that the original author and source are credited and the new work is distributed under the same license as the original.
spellingShingle Genomic Resources Note
Bell, Karen L.
Loeffler, Virginia M.
Brosi, Berry J.
An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)
title An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)
title_full An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)
title_fullStr An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)
title_full_unstemmed An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)
title_short An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding(1)
title_sort rbcl reference library to aid in the identification of plant species mixtures by dna metabarcoding(1)
topic Genomic Resources Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357121/
https://www.ncbi.nlm.nih.gov/pubmed/28337390
http://dx.doi.org/10.3732/apps.1600110
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