Download PDF
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 AffiliationsSupported by: Center for Drug Evaluation and Research, FDA HHSF223201810175
› Further Information
    Permissions and Reprints

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

© 2021. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 

  • References

  • 1 Standley P, Williams L. Labiatae. Fieldiana Bot 1973; 24: 237-317
    PubMedGoogle Scholar
  • 2 Chinese Pharmacopoeia Commission. “Shuanghuanglian keli” in Pharmacopeia of the Peopleʼs Republic of China. China Medicine and Pharmacy. Vol. 1. China Medical Science and Technology Press; 2015: 739
    Google Scholar
  • 3 Li MH, Chen JM, Peng Y, Wu Q, Xiao PG. Investigation of Danshen and related medicinal plants in China. J Ethnopharmacol 2008; 120: 419-426
    CrossrefPubMedGoogle Scholar
  • 4 Zhou LM, Zuo Z, Chow MSS. Danshen: An overview of its chemistry, pharmacology, pharmacokinetics, and clinical use [J]. J Clin Pharmacol 2005; 45: 1345-1359
    CrossrefPubMedGoogle Scholar
  • 5 Mei X, Cao Y, Che Y, Li J, Shang Z, Zhao W, Qiao Y, Zhang J. Danshen: A phytochemical and pharmacological overview. Chin J Nat Med 2019; 17: 59-80
    PubMedGoogle Scholar
  • 6 Xiao XH, Fang QM, Xia WJ. Numerical taxonomy of medicinal Salvia L. and the genuineness of Danshen. J Plant Res Env 1997; 6: 17-21
    PubMedGoogle Scholar
  • 7 Hou YX, Tang HR, Dong XL, Xie WYZ, Chen Q. DNA extraction from Salvia and optimization of RAPD reaction condition. Chin Agric Sci Bull 2008; 24: 72-77
    PubMedGoogle Scholar
  • 8 Wang M, Zhao HX, Wang L, Wang T, Yang RW, Wang XL, Zhou YH, Ding CB, Zhang L. Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences. Gene 2013; 528: 206-215
    PubMedGoogle Scholar
  • 9 Hebert PDN, Cywinska A, Ball SL. Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 2003; 270: 313-321
    CrossrefPubMedGoogle Scholar
  • 10 Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One 2007; 2: e508
    CrossrefPubMedGoogle Scholar
  • 11 CBOL Plant Working Group. A DNA barcode for land plants. Proc Natl Acad Sci U S A 2009; 106: 12794-12797
    CrossrefPubMedGoogle Scholar
  • 12 Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, Leon C. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 2010; 5: e8613
    CrossrefPubMedGoogle Scholar
  • 13 Parveen I, Singh HK, Malik S, Raghuvanshi S, Babbar SB. Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids. Genome 2017; 60: 665-671
    CrossrefPubMedGoogle Scholar
  • 14 de Boer HJ, Ichim MC, Newmaster SG. DNA barcoding and pharmacovigilance of herbal medicines. Drug Saf 2015; 38: 611-620 DOI: 10.1007/s40264-015-0306-8.
    CrossrefPubMedGoogle Scholar
  • 15 Cheng X, Su X, Chen X, Zhao H, Bo C, Xu J, Bai H, Ning K. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: The story for Liuwei Dihuang Wan. Sci Rep 2014; 4: 5147 DOI: 10.1038/srep05147.
    CrossrefPubMedGoogle Scholar
  • 16 de Boer HJ, Ghorbani A, Manzanilla V, Raclariu AC, Kreziou A, Ounjai S, Osathanunkul M, Gravendeel B. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proc Biol Sci 2017; 284: 20171182 DOI: 10.1098/rspb.2017.1182.
    CrossrefPubMedGoogle Scholar
  • 17 Soares S, Grazina L, Costa J, Amaral JS, Oliveira MBPP, Mafra I. Botanical authentication of lavender (Lavandula spp.) honey by a novel DNA-barcoding approach coupled to high resolution melting analysis. Food Control 2018; 86: 367-373 DOI: 10.1016/j.foodcont.2017.11.046.
    CrossrefPubMedGoogle Scholar
  • 18 Huang L, Zheng L, Chen Y, Xue F, Cheng L, Adeloju SB, Chen W. A novel GMO biosensor for rapid ultrasensitive and simultaneous detection of multiple DNA components in GMO products. Biosens Bioelectron 2015; 66: 431-437 DOI: 10.1016/j.bios.2014.12.005.
    CrossrefPubMedGoogle Scholar
  • 19 Li M, Hou XF, Zhang J, Wang SC, Fu Q, He LC. Applications of HPLC/MS in the analysis of traditional Chinese medicines. J Pharm Anal 2011; 1: 81-91 DOI: 10.1016/S2095-1779(11)70015-6.
    CrossrefPubMedGoogle Scholar
  • 20 Parveen I, Gafner S, Techen N, Murch SJ, Khan IA. DNA barcoding for the identification of botanicals in herbal medicine and dietary supplements: strengths and limitations. Planta Med 2016; 82: 1225-1235
    Article in Thieme ConnectPubMedGoogle Scholar
  • 21 Little DP. Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding. Genome 2014; 57: 513-516
    CrossrefPubMedGoogle Scholar
  • 22 Song M, Dong G, Zhang Y, Liu X, Sun W. Identification of processed Chinese medicinal materials using DNA mini-barcoding. Chin J Nat Med 2017; 1: 481-486 DOI: 10.1016/S1875-5364(17)30073-0.
    CrossrefPubMedGoogle Scholar
  • 23 Gao Z, Liu Y, Wang X, Wei X, Han J. DNA mini-barcoding: A derived barcoding method for herbal molecular identification. Front Plant Sci 2019; 10: 987 DOI: 10.3389/fpls.2019.00987.
    CrossrefPubMedGoogle Scholar
  • 24 Han JP, Liu C, Li MH, Shi LC, Song LC, Yao H, Pang XH, Chen SL. Relationship between DNA Barcoding and chemical classification of Salvia medicinal herbs. Chin Herb Med 2010; 2: 16-29
    PubMedGoogle Scholar
  • 25 De Mattia F, Bruni I, Galimberti A, Cattaneo F, Casiraghi M, Labra M. A comparative study of different DNA barcoding markers for the identification of some members of Lamiacaeae. Food Res Int 2011; 44: 693-702
    CrossrefPubMedGoogle Scholar
  • 26 Wang M, Zhao H, Wang L, Wang T, Tang R, Wang X, Zhou Y, Ding C, Zhang L. Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences. Gene 2013; 528: 206-215
    CrossrefPubMedGoogle Scholar
  • 27 Kurian A, Dev SA, Sreekumar VB, Muralidharan EM. The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae). Physiol Mol Biol Plants 2020; 26: 1875-1887
    CrossrefPubMedGoogle Scholar
  • 28 Mason-Gamer RJ, Weil CF, Kello EA. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol 1998; 15: 1658-1673
    CrossrefPubMedGoogle Scholar
  • 29 Miller RE, Rausher MD. Phylogenetic and systematics of Ipomoea (Concolvulaceae) based on ITS and Waxy sequences. Syst Bot 1999; 24: 209-227
    CrossrefPubMedGoogle Scholar
  • 30 Wang Y, Chen Q, Chen T, Zhang J, He W, Liu L, Luo Y, Sun B, Zhang Y, Tang HR, Wang XR. Allopolyploid origin in Rubus (Rosaceae) inferred from nuclear granule-bound starch synthase I (GBSSI) sequences. BMC Plant Biol 2019; 19: 303-316
    CrossrefPubMedGoogle Scholar
  • 31 Parveen I, Techen N, Khan IA. Identification of species in the aromatic spice family Apiaceae using DNA mini-barcodes. Planta Med 2019; 85: 139-144
    Article in Thieme ConnectPubMedGoogle Scholar
  • 32 Lo YT, Li M, Shaw PC. Identification of constituent herbs in ginseng decoctions by DNA markers. Chin Med 2015; 10: 1 DOI: 10.1186/s13020-015-0029-x.
    CrossrefPubMedGoogle Scholar
  • 33 Gao Z, Liu Y, Wang X, Song J, Chen S, Ragupathy S, Han J, Newmaster S. Derivative technology of DNA barcoding (nucleotide signature and SNP double peak methods) detects adulterants and substitution in Chinese patent medicines. Sci Rep 2017; 7: 5858 DOI: 10.1038/s41598-017-05892.
    CrossrefPubMedGoogle Scholar
  • 34 Nicholas KB, Nicholas jr. HB, Deerfield DW. GeneDoc: Analysis and Visualization of Genetic Variation. Embnet news 1997; 4: 14
    PubMedGoogle Scholar
  • 35 White TJ, Bruns T, Lee S, Taylor JW. Amplification and direct Sequencing of fungal ribosomal RNA Genes for Phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, Whit TJ. eds. PCR Protocols: A Guide to Methods and Applications. New York: Academic Press, Inc.; 1990: 315-322
    Google Scholar
  • 36 Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673-4680
    CrossrefPubMedGoogle Scholar
  • 37 Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35: 1547-1549
    CrossrefPubMedGoogle Scholar
  • 38 Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10: 512-526
    PubMedGoogle Scholar
  • 39 Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate Maximum-Likelihood Phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 2010; 59: 307-321
    CrossrefPubMedGoogle Scholar
  • 40 Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001; 17: 754-755
    CrossrefPubMedGoogle Scholar