The complete chloroplast genome sequence of Dendrobium densiflorum and its phylogenetic implications.

Dendrobium is one of the largest genera in Orchidaceae with approximately 1500 species. Many of them have been used as Traditional Chinese Medicine (TCM) for hundreds of years. Here, the first complete chloroplast genome sequence of D. densiflorum was reported and characterized. The complete cpDNA of D. densiflorum is a circular molecule of 153,122 bp, which contains 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Our phylogenetic analysis indicated that the newly sequenced cpDNA of D. densiflorum could be used for the phylogenetic study of Dendrobium species.

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

Owing to its great medicinal and ornamental values, is frequently adulterated with other species on the market. Unfortunately, the utilization of the common DNA markers ITS, ITS2, and + is unable to distinguish from 5 closely related species of it (, , , and ). Here, we compared 63 plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of genes. Furthermore, the intraspecific sequence variability among different species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different species. By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for and its closely related species, indicating that complete plastome sequences can be used to accurately authenticate species.

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

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 species based on their morphological and chemical features. In this study, the plastomes of 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 species, including the newly sequenced plastome of . A total of 19 SNVs that could be used for the authentication of were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the plastome that encompass to , to , to and to . Furthermore, to established a simple and accurate method for the authentication of and its medicinal slices, a total of 127 samples from 20 species including their corresponding medicinal slices (Fengdous) were used in this study. Our results suggest that 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).

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots.

Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots-trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ-should be used in the phylogenetic and identification studies of Dendrobium.

Evaluation of genetic diversity and population structure of Bletilla striata based on SRAP markers / 药学学报

Bletilla striata has been used as traditional Chinese medicine for several centuries. In recent years, the quality and quantity of wild B. striata plants have declined sharply due to habitat deterioration and human over-exploitation. Therefore, it is of great urgency to evaluate and protect B. striata wild plant resource. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to assess the level and pattern of genetic diversity in twelve populations of B. striata. The results showed a high level of genetic diversity (PPB = 90.48%, H = 0.349 4, I = 0.509 6) and moderate genetic differentiation among populations (G(st) = 0.260 9). Based on the unweighted pair-group method with arithmetic average (UPGMA), twelve populations gathered in three clusters. The cluster 1 included four populations. There are Nanjing, Zhenjiang, Xuancheng and Hangzhou. The seven populations which come from Hubei Province, Hunan Province, Jiangxi Province and Guizhou Province belonged to the cluster 2. The cluster 3 only contained Wenshan population. Moreover, Mantel test revealed significant positive correlation between genetic distances and geographic distances (r = 0.632 9; P < 0.000 1). According to the results, we proposed a series of conservation consideration for B. striata.

Applylication of new type combined fragments: nrDNA ITS+ nad 1-intron 2 for identification of Dendrobium species of Fengdous / 药学学报

In this study, 17 kinds of Dendrobium species of Fengdous including 39 individuals were collected from 4 provinces. Mitochondrial gene sequences co I, nad 5, nad 1-intron 2 and chloroplast gene sequences rbcL, matK amd psbA-trnH were amplified from these materials, as well as nrDNA ITS. Furthermore, suitable sequences for identification of Dendrobium species of Fengdous were screened by K-2-P and P-distance. The results showed that during the mentioned 7 sequences, nrDNA ITS, nad 1-intron 2 and psbA-trnH which had a high degree of variability could be used to identify Dendrobium species of Fengdous. However, single fragment could not be used to distinguish D. moniliforme and D. huoshanense. Moreover, compared to other combined fragments, new type combined fragments nrDNA ITS+nad 1-intron 2 was more effective in identifying the original plants of Dendrobium species and could be used to identify D. huoshanense and D. moniliforme. Besides, according to the UPGMA tree constructed with nrDNA ITS+nad 1-intron 2, 3 inspected Dendrobium plants were identified as D. huoshanense, D. moniliforme and D. officinale, respectively. This study identified Dendrobium species of Fengdous by combined fragments nrDNA ITS+nad 1-intron 2 for the first time, which provided a more effective basis for identification of Dendrobium species. And this study will be helpful for regulating the market of Fengdous.