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

Abstract 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 acc...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hoi-Yan Wu, Kwun-Tin Chan, Grace Wing-Chiu But, Pang-Chui Shaw
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/430fb3aee7ab4e5fb995958210e61e0b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:430fb3aee7ab4e5fb995958210e61e0b
record_format	dspace
spelling	oai:doaj.org-article:430fb3aee7ab4e5fb995958210e61e0b2021-12-02T14:11:31ZAssessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification10.1038/s41598-021-82385-z2045-2322https://doaj.org/article/430fb3aee7ab4e5fb995958210e61e0b2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82385-zhttps://doaj.org/toc/2045-2322Abstract 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.Hoi-Yan WuKwun-Tin ChanGrace Wing-Chiu ButPang-Chui ShawNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hoi-Yan Wu Kwun-Tin Chan Grace Wing-Chiu But Pang-Chui Shaw Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
description	Abstract 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.
format	article
author	Hoi-Yan Wu Kwun-Tin Chan Grace Wing-Chiu But Pang-Chui Shaw
author_facet	Hoi-Yan Wu Kwun-Tin Chan Grace Wing-Chiu But Pang-Chui Shaw
author_sort	Hoi-Yan Wu
title	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_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_sort	assessing the reliability of medicinal dendrobium sequences in genbank for botanical species identification
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/430fb3aee7ab4e5fb995958210e61e0b
work_keys_str_mv	AT hoiyanwu assessingthereliabilityofmedicinaldendrobiumsequencesingenbankforbotanicalspeciesidentification AT kwuntinchan assessingthereliabilityofmedicinaldendrobiumsequencesingenbankforbotanicalspeciesidentification AT gracewingchiubut assessingthereliabilityofmedicinaldendrobiumsequencesingenbankforbotanicalspeciesidentification AT pangchuishaw assessingthereliabilityofmedicinaldendrobiumsequencesingenbankforbotanicalspeciesidentification
_version_	1718391837706682368

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

Ejemplares similares