Gentiana is an important but complicated group in Gentianaceae. The genus covers numerous medicinal plants which are difficult to be identified. In the present study, several medicinal species in Gentiana from Yunnan province, including G. rigescens, G.rhodantha, and G. delavayi, were sequenced using the Illumina HiSeq 2500 system. Three complete chloroplast genome sequences were obtained after assembly and annotation. According to several published genome sequences of G. crassicaulis, the DNA super-barcoding of species in Gentiana was preliminarily carried out. The results revealed that chloroplast genomes of the three species were conservative with short lengths(146 944, 148 992, and 148 796 bp, respectively). The genomes encoded 114 genes, including 78 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Furthermore, these medicinal species in Yunnan province were identified using DNA super-barcoding based on chloroplast genomes. The results showed that the Gentiana species could be gathered into monophyletic branches with a high support value(100%). It indicated that DNA super-barcoding possessed obvious advantages in discriminating species in complicated genera. This study is expected to provide a scientific basis for the identification, utilization, and conservation of Gentiana species.
China ; DNA ; Genome, Chloroplast/genetics* ; Gentiana/genetics* ; Phylogeny

Chloroplast genome sequences have comprehensive application prospects in DNA barcoding and chloroplast engineering in traditional Chinese medicine. The complete chloroplast genome of Magnolia officinalis sequenced by high-throughput pyrosequencing and a sequencing procedure was established. Fourteen contigs were obtained after de nove assembly. The sequencing percent of coverage was 99.99%. The chloroplast genome is 160 183 bp in size, and has a typical quadripartite structure with the large (LSC, 88 210 bp) and small copy (SSC, 18 843 bp) regions separated by two copies of an inverted repeat (IRs, 26 565 bp each). chloroplast genes were successfully annotated, of which 17 genes located in each IR region. The chloroplast genome features in Magnolia officinalis are nearly identical to those from other Magnoliid chloroplast genomes. Phylogenetic analyses were performed based on 81 shared coding-genes for a total of 9 Magnolia samples of 5 closely related species. Results showed that distinguishing among species was generally straightforward at the species and population level. This study confirmed the effectiveness of our chloroplast genome sequencing procedure. The chloroplast genome can provide distinguishing differences to help identify Magnolia officinalis and its closely related plants.
Base Sequence ; Chloroplasts ; genetics ; DNA, Chloroplast ; genetics ; Genes, Chloroplast ; Genes, Plant ; Genome, Chloroplast ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; Magnolia ; classification ; genetics ; Phylogeny ; Sequence Analysis, DNA

To compare the characteristic of chloroplast matK gene sequences of different Herba Dendrobium species and to authenticate inspected species, the matK gene sequences of 12 species (including 22 materials) and outgroup were amplified, cloned, and sequenced. Genomic DNA of Dendrobium plants was extracted using modified cetyltrimethyl ammonium bromide (CTAB) method. The matK gene sequences were about 1 410 bp in length. The variable sites were 51 while the parsim-informative sites were 11. There were nucleotides insertions and deletions in some species, in addition to transitions and transversions, such as in D. denneanum and D.chrysotoxum. Interspecies and different populations (varieties) of Dendrobium could be distinguished on phylogeny tree. The average genetic distance was 0.008, and the maximal and minimal genetic distances between Dendrobium species were 0.014 and 0.003, respectively. There were 8-20 variable sites between Dendrobium species. The genetic distance between populations (varieties) was 0.001, and there were 1-5 variable sites. Moreover, the 4 inspected materials were successfully authenticated. The database of chloroplast matK gene sequences of 12 species of Herba Dendrobii and inspected species could be used for the molecular authentication between Dendrobium species and populations. The matK gene sequence could be used as molecular maker for authentication of Herba Dendrobium.
DNA, Chloroplast ; genetics ; DNA, Plant ; genetics ; Dendrobium ; classification ; genetics ; Genes, Chloroplast ; Genes, Plant ; Molecular Sequence Data ; Plants, Medicinal ; genetics ; Sequence Analysis, DNA ; Species Specificity

In this paper, the chloroplast psbK-psbI intergenic spacers of 18 species of Dendrobium and their adulterants were amplified and sequenced, and then the sequence characteristics were analyzed. The sequence lengths of chloroplast psbK-psbI regions of Dendrobium ranged from 474 to 513 bp and the GC contents were 25.4%-27.6%. The variable sites were 71 while the informative sites were 46. The inter-specific genetic distances calculated by Kimura 2-parameter (K2P) of Dendrobium were 0.006 1-0.058 1, with an average of 0.028 4. The K2P genetic distances between Dendrobium species and Bulbophyllum odoratissimum were 0.093 2-0.120 4. The NJ tree showed that the Dendrobium species can be easily differentiated from each other and 6 samples of the inspected Dendrobium species were identified successfully through sequencing the psbK-psbI intergenic spacer. Therefore, the chloroplast psbK-psbI intergenic spacer can be used as a candidate marker to identify Dendrobium species and its adulterants.
Chloroplasts ; DNA, Chloroplast ; genetics ; DNA, Plant ; genetics ; DNA, Ribosomal Spacer ; genetics ; Dendrobium ; classification ; genetics ; Plants, Medicinal ; classification ; genetics

Rhus chinensis is an important economic species, which could provide raw materials for pharmaceutical and industrial dyes. Rhus chinensis is famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. We report here Rhus chinensis chloroplast genomes by de novo sequencing. The results show that the length of Rhus chinensis was 159 082 bp, exhibiting a typical four-part structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The length of LSC and SSC was 85 394 bp and 18 663 bp, respectively. The genomes contained 126 genes, including 88 protein encoding genes, 8 rRNA and 30 tRNA genes. In the chloroplast genome, 61.97% of the sequence were gene coding region. In the sequence of gene encoding region, the vast majority of sequences were protein encoding region, accounting for 86.65%, followed by rRNA (10 620 bp, 10.77%) and tRNA (2 540 bp, 2.58%). In Rhus chinensis chloroplast genome, only 8 genes contain introns, all containing 1 intron except ycf3 gene (2 introns). The Rhus chinensis chloroplast genome contains 755 SSR locies. SSR mainly consists of dinucleotide and mononucleotide, accounting for 60% (453) and 28.74% (217) respectively. The clustering results show that Anacardiaceae were closest to Rhus chinensis, followed by Aceraceae and Sapindaceae. This study provides a molecular basis for the classification of Rhus chinensis.
Genome, Chloroplast ; genetics ; Open Reading Frames ; Phylogeny ; Rhus ; classification ; genetics ; Sequence Analysis, DNA

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.
DNA, Plant ; genetics ; DNA, Ribosomal Spacer ; genetics ; Dendrobium ; classification ; genetics ; Genes, Chloroplast ; Genes, Plant ; Introns ; Plants, Medicinal ; classification ; genetics

The DNA barcoding of traditional Chinese medicine was summarized in this article. Based on analyzing a number of research findings, the authors discussed the possibility of nuclear DNA sequence and chloroplast genes in identifying medicinal materials. ITS was considered to evolve faster, which was used for plant molecular systematics analysis and species identification,while ITS2 was more suitable to identify medicinal materials. So, it is important that we should select suitable DNA sequences as barcodes based on the objective of a study. With the cost reduction of sequencing, identifying medicinal materials by cp-genome barcoding would be applied broadly and effectively in the future.
DNA Barcoding, Taxonomic ; methods ; Genes, Chloroplast ; Medicine, Chinese Traditional ; Plants, Medicinal ; classification ; genetics

OBJECTIVETo investigate the relationship between the variation of chloroplast DNA gene sequences and the geographical origins of Polygonum capitatum in order to provide the molecular evidence for its excellent germplasm resources.

METHODPCR direct sequencing was applied to detect the chloroplast psbA-trnH, trnL-trnF gene sequence of 11 samples collected from 11 populations of P. capitatum.

RESULTThe psbA-trnH gene sequence of P. capitatum from different populations was 402 bp in length, there were 6 variable sites. TrnL-F gene sequence was 875 bp, there were 5 variable sites. The clusters diagram by UPGMA method showed that P. capitatum groups in Yunnan and Guizhou existed a considerable variation.

CONCLUSIONP. capitaturni which is located in the east of Yunnan and the west of Guizhou is helpful of screening the germplasm resources.

Alleles ; Base Sequence ; DNA, Chloroplast ; genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polygonum ; classification ; genetics ; Sequence Alignment ; Sequence Analysis, DNA

The molecular markers(cpSSR, cpSNP and cpIndel) were developed based on the whole genome sequence of Panax notoginseng chloroplast genome, which provide a powerful tool for the evaluation and analysis of the future P. notoginseng germplasm resources. The 89 P. notoginseng samples from 9 groups were used for the experiment, and the data for the study were derived from NCBI and the GenBank numbers were: KJ566590, KP036468, KR021381 and KT001509. Through sequence alignment, 30 polymorphic sites(SNP and Indel) were identified, including 16 cpSNP and 14 cpIndel; cpSNP and cpIndel accounted for far more than the gene region in the intergenic region. The developed cpSSR reached 87-89, the repeat unit was mainly composed of trinucleotide, accounting for 70%-71%, and the dinucleotide was the least, accounting for 7%. Eighteen cpDNA molecular markers were developed, including 7 cpSSR primers, 6 cpIndel primers, and 5 cpSNP primers. The MatK gene and ycf1 primers were chosen as control. According to the results of DNA gel electrophoresis, cpSSR-5, pgcpir019 and pncp08 can be used to distinguish different cultivated populations of P. notoginseng. Among them, cpSSR-5 and pgcpir019 can also be used to distinguish the inter-species resources of ginseng by comprehensive sequence length, population π value and average nucleotide difference. However, pncp08 can only be used to distinguish different populations of P. notoginseng. In addition, the effect of distinguishing the groups of P. notoginseng, which the primer pncp-M(based on the MatK gene) is weaker than the cpSSR-5, pgcpir019 and pncp08.
DNA, Chloroplast/genetics* ; Genetic Markers ; Genetics, Population ; INDEL Mutation ; Panax notoginseng/genetics* ; Polymorphism, Single Nucleotide ; Sequence Alignment

OBJECTIVETo establish a convenient and effective method for the identification of Gynostemma and Cayratia japonica.

METHODEight species, including Gynostemm pentaphyllum, G. pentagynum, G. cardiospermum, G. longipe, G. yixingense, G. laxiflorum, G. guangxiense and C. japonica were investigated through PCR - RFLP of six chloroplast DNA fragments. The six gene fragments were digested by six restriction endonuclease respectively, including Taq I, Hpa II, EcoR I, Rsa I, Hha I, Hind III.

RESULTSeven species of Gynostemma and their adulterant could be identified by trnK1f-trnK2r and Rsa.

CONCLUSIONPCR - RFLP provides a quick, reliable molecular marker technique for identification of Cynostemma and their adulterant Cayratia japonica.

DNA, Chloroplast ; genetics ; DNA, Plant ; genetics ; Gynostemma ; classification ; genetics ; Polymerase Chain Reaction ; methods ; Polymorphism, Restriction Fragment Length ; genetics ; Vitaceae ; classification ; genetics