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Planta Med 2022; 88(12): 985-993
DOI: 10.1055/a-1618-6496
Natural Product Chemistry and Analytical Studies
Original Papers

The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

Iffat Parveen 
1   National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
,
Natascha Techen 
1   National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
,
Sara M. Handy 
2   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, MD, USA
,
Jing Li
3   Botanical Review Team, Immediate Office, Office of New Drug Product, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
,
Charles Wu
3   Botanical Review Team, Immediate Office, Office of New Drug Product, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
,
Amar G. Chittiboyina
1   National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
,
Ikhlas A. Khan
1   National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
4   Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, USA
› Author Affiliations
Supported by: Center for Drug Evaluation and Research, FDA HHSF223201810175
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Abstract

Morphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 – 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.

Key words

Salvia - Lamiaceae - DNA barcoding - Mini-barcodes - GBSS1 - ITS - Salvia apiana - Salvia divinorum - Salvia hispanica - Salvia mellifera - Salvia miltiorrhiza - Salvia officinalis - Salvia sclarea

Supporting Information

    Table S1: The aligned GBSS1 sequences were analyzed using the Kimura-2-parameter model, and the number of base substitutions per site from between sequences is shown. The analysis involved 20 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All ambiguous positions were removed for each sequence pair (pairwise deletion option). There were a total of 236 positions in the final dataset. Distance analyses were conducted in MEGAX.

  • Excel file

    Table S2: The aligned ITS2 sequences were analyzed using the Kimura-2-parameter model, and the number of base substitutions per site from between sequences is shown. The analysis involved 14 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All ambiguous positions were removed for each sequence pair (pairwise deletion option). There were a total of 365 positions in the final dataset. Distance analyses were conducted in MEGAX.

  • Excel file

    Table S3: The GBSS1 sequences obtained after Sanger sequencing were assembled and trimmed in DNASTAR Lasergene software. Listed are the 20 GBSS1 final sequences as DNA mini-barcodes for different Salvia species.

  • PDF file


Publication History

Received: 29 April 2021

Accepted after revision: 26 August 2021

Article published online:
20 September 2021

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