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Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum
Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the hi...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9690082/ https://www.ncbi.nlm.nih.gov/pubmed/36421768 http://dx.doi.org/10.3390/genes13112093 |
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author | Wu, Xin-Yi Li, Ting-Zhang Zheng, Fang Chen, Jian-Bing Yan, Yue-Hong Huang, Jiu-Xiang |
author_facet | Wu, Xin-Yi Li, Ting-Zhang Zheng, Fang Chen, Jian-Bing Yan, Yue-Hong Huang, Jiu-Xiang |
author_sort | Wu, Xin-Yi |
collection | PubMed |
description | Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 D. catenatum provenances. In this study, 371.18 Gb clean data were obtained, and 655,057 high-quality SNPs were selected after their filtration. We used phylogenetic tree, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 109 accessions. We found that D. catenatum could be divided into two groups, and each group was closely related to the distribution of the sampling sites. At the population level, the average nucleotide diversity (π) of the D. catenatum population mutation parameters was 0.1584 and the expected heterozygosity (H(E)) was 0.1575. The GXLPTP07 accessions showed the highest genetic diversity in terms of the private allele number, observed heterozygosity, and nucleotide diversity. The Mantel test showed a significant positive correlation between the genetic and geographic distances among the overall distribution. A genetic information database of D. catenatum was established, which confirmed that RAD-seq technology has the potential to be applied in the identification of medicinal Dendrobium of different origins. |
format | Online Article Text |
id | pubmed-9690082 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96900822022-11-25 Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum Wu, Xin-Yi Li, Ting-Zhang Zheng, Fang Chen, Jian-Bing Yan, Yue-Hong Huang, Jiu-Xiang Genes (Basel) Article Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 D. catenatum provenances. In this study, 371.18 Gb clean data were obtained, and 655,057 high-quality SNPs were selected after their filtration. We used phylogenetic tree, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 109 accessions. We found that D. catenatum could be divided into two groups, and each group was closely related to the distribution of the sampling sites. At the population level, the average nucleotide diversity (π) of the D. catenatum population mutation parameters was 0.1584 and the expected heterozygosity (H(E)) was 0.1575. The GXLPTP07 accessions showed the highest genetic diversity in terms of the private allele number, observed heterozygosity, and nucleotide diversity. The Mantel test showed a significant positive correlation between the genetic and geographic distances among the overall distribution. A genetic information database of D. catenatum was established, which confirmed that RAD-seq technology has the potential to be applied in the identification of medicinal Dendrobium of different origins. MDPI 2022-11-10 /pmc/articles/PMC9690082/ /pubmed/36421768 http://dx.doi.org/10.3390/genes13112093 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Wu, Xin-Yi Li, Ting-Zhang Zheng, Fang Chen, Jian-Bing Yan, Yue-Hong Huang, Jiu-Xiang Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum |
title | Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum |
title_full | Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum |
title_fullStr | Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum |
title_full_unstemmed | Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum |
title_short | Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum |
title_sort | population diversity analysis provide insights into provenance identification of dendrobium catenatum |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9690082/ https://www.ncbi.nlm.nih.gov/pubmed/36421768 http://dx.doi.org/10.3390/genes13112093 |
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