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Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia

DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains...

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Autores principales: Xu, Songzhi, Li, Dezhu, Li, Jianwu, Xiang, Xiaoguo, Jin, Weitao, Huang, Weichang, Jin, Xiaohua, Huang, Luqi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300225/
https://www.ncbi.nlm.nih.gov/pubmed/25602282
http://dx.doi.org/10.1371/journal.pone.0115168
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author Xu, Songzhi
Li, Dezhu
Li, Jianwu
Xiang, Xiaoguo
Jin, Weitao
Huang, Weichang
Jin, Xiaohua
Huang, Luqi
author_facet Xu, Songzhi
Li, Dezhu
Li, Jianwu
Xiang, Xiaoguo
Jin, Weitao
Huang, Weichang
Jin, Xiaohua
Huang, Luqi
author_sort Xu, Songzhi
collection PubMed
description DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera.
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spelling pubmed-43002252015-01-30 Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia Xu, Songzhi Li, Dezhu Li, Jianwu Xiang, Xiaoguo Jin, Weitao Huang, Weichang Jin, Xiaohua Huang, Luqi PLoS One Research Article DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera. Public Library of Science 2015-01-20 /pmc/articles/PMC4300225/ /pubmed/25602282 http://dx.doi.org/10.1371/journal.pone.0115168 Text en © 2015 Xu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Xu, Songzhi
Li, Dezhu
Li, Jianwu
Xiang, Xiaoguo
Jin, Weitao
Huang, Weichang
Jin, Xiaohua
Huang, Luqi
Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia
title Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia
title_full Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia
title_fullStr Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia
title_full_unstemmed Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia
title_short Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia
title_sort evaluation of the dna barcodes in dendrobium (orchidaceae) from mainland asia
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300225/
https://www.ncbi.nlm.nih.gov/pubmed/25602282
http://dx.doi.org/10.1371/journal.pone.0115168
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