Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

Antariksh Tyagi, Sumit K Bag, Virendra Shukla, Sribash Roy and Rakesh Tuli

PLOS ONE, 2010, vol. 5, issue 8, 1-9

Abstract: Background: DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings: A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance: Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies.

Date: 2010
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0012330

DOI: 10.1371/journal.pone.0012330

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