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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences
Nitin Mantri1, Alexandra Olarte, Chun Guang Li
1School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia. nitin.mantri@rmit.edu.au
Plos One
|April 13, 2012
Summary
A new Asterid-specific microarray accurately identifies medicinal plants, preventing adulteration. This DNA fingerprinting method uses chloroplast genes and is highly efficient for species identification.
Area of Science:
- Botany
- Genomics
- Molecular Biology
Background:
- Asterids represent a major plant clade with significant medicinal value.
- Plant adulteration due to misidentification is a critical issue in the medicinal plant industry.
- Developing reliable methods for identifying medicinal species is essential.
Purpose of the Study:
- To construct and validate a DNA microarray for precise fingerprinting of medicinally important Asterid species.
- To address the challenge of adulteration and misidentification in the herbal plant industry.
- To identify novel genetic markers for plant identification.
Main Methods:
- Utilized Subtracted Diversity Array (SDA) technique.
- Constructed an Asterid-specific array using subtracted genomic DNA fragments.
- Validated the array by hybridizing DNA from 25 Asterid species.
Main Results:
- Achieved high subtraction efficiency (99.5%) in array construction.
- Successfully differentiated all 25 tested Asterid species, including those not used in array development.
- Identified numerous species-specific probes, including novel loci and probes from chloroplast genes (e.g., atpB, rpoB, ndh).
- Characterized 37 polymorphic probes via sequencing.
Conclusions:
- The Subtracted Diversity Array (SDA) technique is highly effective for species fingerprinting, even with limited genomic data.
- The Asterid-specific array provides accurate identification of medicinal plant species, crucial for quality control.
- Validated the utility of chloroplast genes for plant DNA bar-coding and identified new markers for phylogenetic and fingerprinting applications.
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