Abstract
Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.
Highlights
Dendrobium is one of the three largest genera of the Orchidaceae family and comprises more than 1,000 species distributed throughout the Asian tropical and subtropical regions as well as Oceania, with 78 species of this genus recorded in China alone [1]
We first investigated the levels of intragenomic variation in the internal transcribed spacer 2 (ITS2) regions of 18 Dendrobium medicinal materials
Major variants representing more than 90% of ITS2 sequences were found in D. crepidatum (p1-1), D. aphyllum (P2-1), D. devonianum (p31), D. officinale (p4-1), D. trigonopus (p16-1), D. gratiosissimum (p15-1), D. capillipes (p13-1), and D. denneanum (p5-1), which were present at 99.27%, 95.87%, 95.43%, 93.89%, 93.34%, 93.23%, 93.03%, and 91.50% of total sequences, respectively
Summary
Dendrobium is one of the three largest genera of the Orchidaceae family and comprises more than 1,000 species distributed throughout the Asian tropical and subtropical regions as well as Oceania, with 78 species of this genus recorded in China alone [1]. Dendrobium is well known for its medical value. One of the earliest records of Orchidaceae plants in ancient Chinese literature is Shen Nong’s classic herbal text written approximately 1,500 years ago. 33 species of Dendrobium are used as clinical medications [2], including Dendrobium officinale, known as “Tie Pi Feng Dou,” and Dendrobium nobile, known as “Jin chai shi hu,” as described in the Chinese Pharmacopoeia. Large numbers of Dendrobium species are needed for both the flower and medicinal markets
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