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Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification

DNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and...

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Autores principales: Wu, Hoi-Yan, Chan, Kwun-Tin, But, Grace Wing-Chiu, Shaw, Pang-Chui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873228/
https://www.ncbi.nlm.nih.gov/pubmed/33564041
http://dx.doi.org/10.1038/s41598-021-82385-z
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author Wu, Hoi-Yan
Chan, Kwun-Tin
But, Grace Wing-Chiu
Shaw, Pang-Chui
author_facet Wu, Hoi-Yan
Chan, Kwun-Tin
But, Grace Wing-Chiu
Shaw, Pang-Chui
author_sort Wu, Hoi-Yan
collection PubMed
description DNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.
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spelling pubmed-78732282021-02-11 Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification Wu, Hoi-Yan Chan, Kwun-Tin But, Grace Wing-Chiu Shaw, Pang-Chui Sci Rep Article DNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases. Nature Publishing Group UK 2021-02-09 /pmc/articles/PMC7873228/ /pubmed/33564041 http://dx.doi.org/10.1038/s41598-021-82385-z Text en © The Author(s) 2021 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/.
spellingShingle Article
Wu, Hoi-Yan
Chan, Kwun-Tin
But, Grace Wing-Chiu
Shaw, Pang-Chui
Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
title Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
title_full Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
title_fullStr Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
title_full_unstemmed Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
title_short Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
title_sort assessing the reliability of medicinal dendrobium sequences in genbank for botanical species identification
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873228/
https://www.ncbi.nlm.nih.gov/pubmed/33564041
http://dx.doi.org/10.1038/s41598-021-82385-z
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