The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis

The loss of forests is a major environmental, social, and economic problem. The disappearance has been occurring to an extreme degree in many parts of Southeast Asia, including Thailand. Logging and clearing of forests for agriculture, cash crops, and food production has destroyed much of the tropic...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Maslin Osathanunkul, Panagiotis Madesis
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	tropical forests High Resolution Melting analysis species identification primer design Dipterocarpaceae Fagaceae Plant ecology QK900-989
Acceso en línea:	https://doaj.org/article/b71e08c4fc194f9f8a85ccc1e5b0fc86
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b71e08c4fc194f9f8a85ccc1e5b0fc86
record_format	dspace
spelling	oai:doaj.org-article:b71e08c4fc194f9f8a85ccc1e5b0fc862021-11-25T17:37:34ZThe Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis10.3390/f121114661999-4907https://doaj.org/article/b71e08c4fc194f9f8a85ccc1e5b0fc862021-10-01T00:00:00Zhttps://www.mdpi.com/1999-4907/12/11/1466https://doaj.org/toc/1999-4907The loss of forests is a major environmental, social, and economic problem. The disappearance has been occurring to an extreme degree in many parts of Southeast Asia, including Thailand. Logging and clearing of forests for agriculture, cash crops, and food production has destroyed much of the tropical forests in Thailand. Floristic inventory could provide essential information for forest conservation but species identification as a part of inventory creating could be challenging in some cases. Barcode DNA coupled with High Resolution Melting analysis (Bar-HRM) was used here in aiding species identification of plant in Dipterocarpaceae (<i>Dipterocarpus alatus</i>, <i>D. costatu</i>, <i>D. intricatus</i>, <i>D. obtusifolius</i>, <i>Hopea ferrea</i>, <i>H. odorata</i>, <i>Shorea guiso</i>, <i>S. obtuse</i>, <i>S. roxburghii</i>, and <i>S. siamensis</i>) and Fagaceae (<i>Castanopsis echinocarpa</i>, <i>C. inermis</i>, <i>Lithocarpus wallichianus</i>, <i>Quercus aliena</i> and <i>Q. oidocarpa</i>) families. Two main experiments were conducted including: (1) a comparing method for primer design and (2) testing the robustness of the Bar-HRM by trying to identify tree samples that did not have sequences in the GenBank. In experiment 1, the manual design primer pair was found to be the best fit for the work. Of key importance is finding the primers which give the most nucleotide variations within the generated amplicon; this is a parameter that cannot be set in any web-based tools. Next, in experiment 2, Bar-HRM using primers of ITS1 and ITS2 regions were able to discriminate all 10 tested tree species without any problem, even when there were no sequences of the samples to be analysed before performing the HRM. Here, Bar-HRM poses potential to be a game-changer in tropical forest conservation, as it will be useful for species identification.Maslin OsathanunkulPanagiotis MadesisMDPI AGarticletropical forestsHigh Resolution Melting analysisspecies identificationprimer designDipterocarpaceaeFagaceaePlant ecologyQK900-989ENForests, Vol 12, Iss 1466, p 1466 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	tropical forests High Resolution Melting analysis species identification primer design Dipterocarpaceae Fagaceae Plant ecology QK900-989
spellingShingle	tropical forests High Resolution Melting analysis species identification primer design Dipterocarpaceae Fagaceae Plant ecology QK900-989 Maslin Osathanunkul Panagiotis Madesis The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis
description	The loss of forests is a major environmental, social, and economic problem. The disappearance has been occurring to an extreme degree in many parts of Southeast Asia, including Thailand. Logging and clearing of forests for agriculture, cash crops, and food production has destroyed much of the tropical forests in Thailand. Floristic inventory could provide essential information for forest conservation but species identification as a part of inventory creating could be challenging in some cases. Barcode DNA coupled with High Resolution Melting analysis (Bar-HRM) was used here in aiding species identification of plant in Dipterocarpaceae (<i>Dipterocarpus alatus</i>, <i>D. costatu</i>, <i>D. intricatus</i>, <i>D. obtusifolius</i>, <i>Hopea ferrea</i>, <i>H. odorata</i>, <i>Shorea guiso</i>, <i>S. obtuse</i>, <i>S. roxburghii</i>, and <i>S. siamensis</i>) and Fagaceae (<i>Castanopsis echinocarpa</i>, <i>C. inermis</i>, <i>Lithocarpus wallichianus</i>, <i>Quercus aliena</i> and <i>Q. oidocarpa</i>) families. Two main experiments were conducted including: (1) a comparing method for primer design and (2) testing the robustness of the Bar-HRM by trying to identify tree samples that did not have sequences in the GenBank. In experiment 1, the manual design primer pair was found to be the best fit for the work. Of key importance is finding the primers which give the most nucleotide variations within the generated amplicon; this is a parameter that cannot be set in any web-based tools. Next, in experiment 2, Bar-HRM using primers of ITS1 and ITS2 regions were able to discriminate all 10 tested tree species without any problem, even when there were no sequences of the samples to be analysed before performing the HRM. Here, Bar-HRM poses potential to be a game-changer in tropical forest conservation, as it will be useful for species identification.
format	article
author	Maslin Osathanunkul Panagiotis Madesis
author_facet	Maslin Osathanunkul Panagiotis Madesis
author_sort	Maslin Osathanunkul
title	The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis
title_short	The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis
title_full	The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis
title_fullStr	The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis
title_full_unstemmed	The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis
title_sort	identification of several dipterocarpaceae and fagaceae trees by barcode dna coupled with high-resolution melting analysis
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/b71e08c4fc194f9f8a85ccc1e5b0fc86
work_keys_str_mv	AT maslinosathanunkul theidentificationofseveraldipterocarpaceaeandfagaceaetreesbybarcodednacoupledwithhighresolutionmeltinganalysis AT panagiotismadesis theidentificationofseveraldipterocarpaceaeandfagaceaetreesbybarcodednacoupledwithhighresolutionmeltinganalysis AT maslinosathanunkul identificationofseveraldipterocarpaceaeandfagaceaetreesbybarcodednacoupledwithhighresolutionmeltinganalysis AT panagiotismadesis identificationofseveraldipterocarpaceaeandfagaceaetreesbybarcodednacoupledwithhighresolutionmeltinganalysis
_version_	1718412188123660288

The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis

Ejemplares similares