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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.

Barcoding theDendrobium(Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2