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The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain
BACKGROUND: Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629101/ https://www.ncbi.nlm.nih.gov/pubmed/37936056 http://dx.doi.org/10.1186/s12870-023-04513-3 |
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author | Wang, Weijie Chen, Baixu Ma, Ruoke Qiao, Mengji Fu, Yunlin |
author_facet | Wang, Weijie Chen, Baixu Ma, Ruoke Qiao, Mengji Fu, Yunlin |
author_sort | Wang, Weijie |
collection | PubMed |
description | BACKGROUND: Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. RESULTS: Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. CONCLUSIONS: The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04513-3. |
format | Online Article Text |
id | pubmed-10629101 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-106291012023-11-08 The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain Wang, Weijie Chen, Baixu Ma, Ruoke Qiao, Mengji Fu, Yunlin BMC Plant Biol Research BACKGROUND: Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. RESULTS: Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. CONCLUSIONS: The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04513-3. BioMed Central 2023-11-07 /pmc/articles/PMC10629101/ /pubmed/37936056 http://dx.doi.org/10.1186/s12870-023-04513-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Wang, Weijie Chen, Baixu Ma, Ruoke Qiao, Mengji Fu, Yunlin The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain |
title | The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain |
title_full | The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain |
title_fullStr | The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain |
title_full_unstemmed | The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain |
title_short | The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain |
title_sort | dna barcode identification of dalbergia odorifera t. chen and dalbergia tonkinensis prain |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629101/ https://www.ncbi.nlm.nih.gov/pubmed/37936056 http://dx.doi.org/10.1186/s12870-023-04513-3 |
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