Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice (Huoshan Fengdou)

Abstract

Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine (TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants (SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3′trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices (Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system (ARMS).

Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

“…The accurate identification of medicinal plants is essential to their safe utilization and genetic resource conservation. However, Dendrobium species have been documented to be difficult for discrimination analysis due to their similar appearance and tissue structure 9 , 10 , 11 . Among them, D. officinale and its closely related species are a particularly difficult group for identification studies and phylogenetic analyses due to the overlapping morphological variations 14 , 54 , 55 , complex evolutionary histories 15 , and the lack of effective molecular markers.…”

“…Dendrobium species are notoriously difficult to identify due to their similar appearance and tissue structure 9 , 10 , 11 . Usually, their identification relies heavily on morphological methods as well as phytochemical approaches such as capillary electrophoresis (CE) 12 and high-pressure liquid chromatography (HPLC) 13 .…”

Gene Losses and Variations in Chloroplast Genome of Parasitic Plant Macrosolen and Phylogenetic Relationships within Santalales

“…A typical chloroplast genome of most angiosperms consists of four parts, namely a pair of inverted repeats (IRa and IRb), a large single-copy (LSC) region and a small single-copy (SSC) region [20]. The chloroplast genome sequences are highly conserved in gene order and content [21], and they are thus ideal research models for the study of molecular markers [22,23], species identification [24,25,26], and species evolution [27].…”

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis

“…But, the similar appearance and tissue structure among these species have led to notorious difficulties to identify them. The drug markets of Dendrobium species from one place are always complex with those from other places (Niu et al 2018; Xu et al 2014). Therefore, it is critical and important to precisely differentiate the wild and cultivated Dendrobiums plants at specie level for guaranteeing their quality and safety in practical use, as well as genetic resource conservation.…”