The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

Abstract DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identificat...

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Autores principales:	Huili Li, Wenjun Xiao, Tie Tong, Yongliang Li, Meng Zhang, Xiaoxia Lin, Xiaoxiao Zou, Qun Wu, Xinhong Guo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/38104a26370c4ece961d8391901b3f56
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spelling	oai:doaj.org-article:38104a26370c4ece961d8391901b3f562021-12-02T14:12:48ZThe specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants10.1038/s41598-021-81087-w2045-2322https://doaj.org/article/38104a26370c4ece961d8391901b3f562021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-81087-whttps://doaj.org/toc/2045-2322Abstract DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.Huili LiWenjun XiaoTie TongYongliang LiMeng ZhangXiaoxia LinXiaoxiao ZouQun WuXinhong GuoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Huili Li Wenjun Xiao Tie Tong Yongliang Li Meng Zhang Xiaoxia Lin Xiaoxiao Zou Qun Wu Xinhong Guo The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants
description	Abstract DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.
format	article
author	Huili Li Wenjun Xiao Tie Tong Yongliang Li Meng Zhang Xiaoxia Lin Xiaoxiao Zou Qun Wu Xinhong Guo
author_facet	Huili Li Wenjun Xiao Tie Tong Yongliang Li Meng Zhang Xiaoxia Lin Xiaoxiao Zou Qun Wu Xinhong Guo
author_sort	Huili Li
title	The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants
title_short	The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants
title_full	The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants
title_fullStr	The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants
title_full_unstemmed	The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants
title_sort	specific dna barcodes based on chloroplast genes for species identification of orchidaceae plants
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/38104a26370c4ece961d8391901b3f56
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The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

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