Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.

<h4>Background</h4>Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construc...

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Autores principales:	Nitin Mantri, Alexandra Olarte, Chun Guang Li, Charlie Xue, Edwin C K Pang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e019849e21bd4a10bc5fc136f123d7f6
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spelling	oai:doaj.org-article:e019849e21bd4a10bc5fc136f123d7f62021-11-18T07:22:53ZFingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.1932-620310.1371/journal.pone.0034873https://doaj.org/article/e019849e21bd4a10bc5fc136f123d7f62012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22496874/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.<h4>Methodology/principal findings</h4>Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants.<h4>Conclusions/significance</h4>Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve existing discrepancies in phylogenetics and fingerprinting of plants.Nitin MantriAlexandra OlarteChun Guang LiCharlie XueEdwin C K PangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e34873 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nitin Mantri Alexandra Olarte Chun Guang Li Charlie Xue Edwin C K Pang Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.
description	<h4>Background</h4>Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.<h4>Methodology/principal findings</h4>Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants.<h4>Conclusions/significance</h4>Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve existing discrepancies in phylogenetics and fingerprinting of plants.
format	article
author	Nitin Mantri Alexandra Olarte Chun Guang Li Charlie Xue Edwin C K Pang
author_facet	Nitin Mantri Alexandra Olarte Chun Guang Li Charlie Xue Edwin C K Pang
author_sort	Nitin Mantri
title	Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.
title_short	Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.
title_full	Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.
title_fullStr	Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.
title_full_unstemmed	Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.
title_sort	fingerprinting the asterid species using subtracted diversity array reveals novel species-specific sequences.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/e019849e21bd4a10bc5fc136f123d7f6
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Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.

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