Dataset Information

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

ABSTRACT: BACKGROUND: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. METHODOLOGY/PRINCIPAL FINDINGS: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. CONCLUSIONS/SIGNIFICANCE: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.

SUBMITTER: Mantri N

PROVIDER: S-EPMC3322160 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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

Mantri Nitin N Olarte Alexandra A Li Chun Guang CG Xue Charlie C Pang Edwin C K EC

PloS one 20120409 4

<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- ...[more]

PMID: 22496874

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Dataset Information

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

Publications

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

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