A Phylogenetic Analysis Based on Whole Genome Re-Sequencing of 41 Dendrobium Species

The genus Dendrobium (Orchidaceae) is highly renowned for its great medicinal and ornamental values. However, due to morphological similarities among closely related taxa within this genus, certain species are frequently subject to misidentification and adulteration in the market. Traditional morphological taxonomy and limited DNA markers prove challenging in effectively differentiating among them. Here, we generated an extensive single nucleotide polymorphism (SNP) dataset through whole genome re-sequencing (WGRS) of 41 Dendrobium species to evaluate its effectiveness in species identification. The phylogenetic relationships of 41 Dendrobium species were explored based on the SNP dataset, and then divergence times at each node were estimated. We found that the whole genome re-sequencing method achieved a 100% identification rate for all 41 species examined, indicating that whole genome re-sequencing could be employed to accurately authenticate Dendrobium species. Furthermore, phylogenetic analysis revealed that the sect. Dendrobium was polyphyletic. In addition, the divergence time analysis suggested that Dendrobium originated since the Oligocene. These findings provide valuable genetic data resources for further systematic studies of the rare and endangered Dendrobium species.