Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region

Xin Ye Ma, Cai Xiang Xie, Chang Liu, Jing Yuan Song, Hui Yao, Kun Luo, Yingjie Zhu, Ting Gao, Xiao Hui Pang, Jun Qian, Shi Lin Chen

Research output: Contribution to journalComment/debate

45 Citations (Scopus)

Abstract

Medicinal pteridophytes are an important group used in traditional Chinese medicine; however, there is no simple and universal way to differentiate various species of this group by morphological traits. A novel technology termed "DNA barcoding" could discriminate species by a standard DNA sequence with universal primers and sufficient variation. To determine whether DNA barcoding would be effective for differentiating pteridophyte species, we first analyzed five DNA sequence markers (psbA-trnH intergenic region, rbcL, rpoB, rpoC1, and matK) using six chloroplast genomic sequences from GeneBank and found psbA-trnH intergenic region the best candidate for availability of universal primers. Next, we amplified the psbA-trnH region from 79 samples of medicinal pteridophyte plants. These samples represented 51 species from 24 families, including all the authentic pteridophyte species listed in the Chinese pharmacopoeia (2005 version) and some commonly used adulterants. We found that the sequence of the psbA-trnH intergenic region can be determined with both high polymerase chain reaction (PCR) amplification efficiency (94.1%) and high direct sequencing success rate (81.3%). Combined with GeneBank data (54 species cross 12 pteridophyte families), species discriminative power analysis showed that 90.2% of species could be separated/identified successfully by the TaxonGap method in conjunction with the Basic Local Alignment Search Tool 1 (BLAST1) method. The TaxonGap method results further showed that, for 37 out of 39 separable species with at least two samples each, between-species variation was higher than the relevant within-species variation. Thus, the psbA-trnH intergenic region is a suitable DNA marker for species identification in medicinal pteridophytes.

Original languageEnglish (US)
Pages (from-to)1919-1924
Number of pages6
JournalBiological and Pharmaceutical Bulletin
Volume33
Issue number11
DOIs
StatePublished - Nov 19 2010
Externally publishedYes

Fingerprint

Intergenic DNA
Chloroplasts
Genetic Markers
Pharmacopoeias
DNA
Chinese Traditional Medicine
Medicinal Plants
Technology
Polymerase Chain Reaction

Keywords

  • Medicinal pteridophyte
  • Psba-trnH intergenic region
  • Species identification

ASJC Scopus subject areas

  • Pharmacology
  • Pharmaceutical Science

Cite this

Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region. / Ma, Xin Ye; Xie, Cai Xiang; Liu, Chang; Song, Jing Yuan; Yao, Hui; Luo, Kun; Zhu, Yingjie; Gao, Ting; Pang, Xiao Hui; Qian, Jun; Chen, Shi Lin.

In: Biological and Pharmaceutical Bulletin, Vol. 33, No. 11, 19.11.2010, p. 1919-1924.

Research output: Contribution to journalComment/debate

Ma, XY, Xie, CX, Liu, C, Song, JY, Yao, H, Luo, K, Zhu, Y, Gao, T, Pang, XH, Qian, J & Chen, SL 2010, 'Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region', Biological and Pharmaceutical Bulletin, vol. 33, no. 11, pp. 1919-1924. https://doi.org/10.1248/bpb.33.1919
Ma, Xin Ye ; Xie, Cai Xiang ; Liu, Chang ; Song, Jing Yuan ; Yao, Hui ; Luo, Kun ; Zhu, Yingjie ; Gao, Ting ; Pang, Xiao Hui ; Qian, Jun ; Chen, Shi Lin. / Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region. In: Biological and Pharmaceutical Bulletin. 2010 ; Vol. 33, No. 11. pp. 1919-1924.
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AU - Liu, Chang

AU - Song, Jing Yuan

AU - Yao, Hui

AU - Luo, Kun

AU - Zhu, Yingjie

AU - Gao, Ting

AU - Pang, Xiao Hui

AU - Qian, Jun

AU - Chen, Shi Lin

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N2 - Medicinal pteridophytes are an important group used in traditional Chinese medicine; however, there is no simple and universal way to differentiate various species of this group by morphological traits. A novel technology termed "DNA barcoding" could discriminate species by a standard DNA sequence with universal primers and sufficient variation. To determine whether DNA barcoding would be effective for differentiating pteridophyte species, we first analyzed five DNA sequence markers (psbA-trnH intergenic region, rbcL, rpoB, rpoC1, and matK) using six chloroplast genomic sequences from GeneBank and found psbA-trnH intergenic region the best candidate for availability of universal primers. Next, we amplified the psbA-trnH region from 79 samples of medicinal pteridophyte plants. These samples represented 51 species from 24 families, including all the authentic pteridophyte species listed in the Chinese pharmacopoeia (2005 version) and some commonly used adulterants. We found that the sequence of the psbA-trnH intergenic region can be determined with both high polymerase chain reaction (PCR) amplification efficiency (94.1%) and high direct sequencing success rate (81.3%). Combined with GeneBank data (54 species cross 12 pteridophyte families), species discriminative power analysis showed that 90.2% of species could be separated/identified successfully by the TaxonGap method in conjunction with the Basic Local Alignment Search Tool 1 (BLAST1) method. The TaxonGap method results further showed that, for 37 out of 39 separable species with at least two samples each, between-species variation was higher than the relevant within-species variation. Thus, the psbA-trnH intergenic region is a suitable DNA marker for species identification in medicinal pteridophytes.

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