DNA barcoding analysis: quality control of published DNA sequences

DNA barcoding methods are an important addition to the identification and quality testing of herbal medicines when applied correctly [1].

A robust and complementary method in identifying plant materials is the use of DNA barcoding which, when applied within a quality framework [2], forms a key component of the successful authentication of herbal drugs [3], [4]. However, as with any methodology, high quality reference information is required. The open access nature of DNA databases has provided an abundance of sequence data but has also created the issue of incorrectly labelled sequences and unverified data. In this study these issues are highlighted via an investigation of published Mentha spicata L. sequences, and a guideline for the quality assessment of sequence data introduced.

Data were collected from two online databases relating to M. spicata and two barcode regions, the ITS2 and trnH-psbA. As would be expected, variation was found between the published sequences. However, several sequences appeared to be mislabelled, and on investigation of some accompanying manuscripts a link to unverified material was shown.

To quality control this issue, several steps were taken to critically evaluate sequence data. This was then further developed into a guideline for the assessment of published sequences [Fig. 1] which can be used for any investigation.

It is clear that publicly available sequences should be subject to such scrutiny and quality control for best practice. Utilising this method, an operator can gain a higher level of confidence in the published sequences used and a harmonised approach during data analysis.

Fig. 1 Quality control method used to assess publicly available DNA sequence data.

• References

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• 2 Sgamma T, Lockie-Williams C, Kreuzer M, Williams S, Scheyhing U, Koch E. et al. DNA Barcoding for Industrial Quality Assurance. Planta Med 2017; 83: 14-15
• 3 Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R. et al. DNA barcoding: An efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol J Jan 2016; 14 (01) 8-21
• 4 Kazi T, Hussain N, Bremner P, Slater A, Howard C. The application of a DNA-based identification technique to over-the-counter herbal medicines. Fitoterapia Jun 2013; 87: 27-30