Analysis of the chloroplast genome of Incarvillea younghusbandii Sprague / 生物工程学报

Incarvillea younghusbandii Sprague is a traditional tonic herb. The roots are used as herbal medicine for nourishing and strengthening, as well as treating postpartum milk deficiency and weakness. In this study, the chloroplast genome of I. younghusbandii was sequenced and assembled by the high-throughput sequencing technology. The sequence characteristics, sequence repeats, codon usage bias, phylogenetic relationships and estimated divergence time of I. younghusbandii were analyzed. The 159 323 bp sequence contained a large single copy (80 197 bp), a small single copy (9 030 bp) and two inverted repeat sequences (35 048 bp). It contained 120 genes, including 77 protein coding genes, 8 ribosomal RNA genes and 35 transfer RNA genes. AAA was the most frequent codon in the chloroplast coding sequence of I. younghusbandii. A total of 42 simple sequence repeats were identified in the chloroplast genome. Phylogenetic analysis revealed I. younghusbandii was mostly like its taxonomically close relative Incarvillea compacta. The divergence between I. younghusbandii and I. compacta was dated to 4.66 million years ago. This study was significant for the scientific conservation and development of resources related to I. compacta. It also provides a basic genetic resource for the subsequent species identification of the genus Incarvillea, and the population genetic diversity study of Bignoniaceae.

DNA super-barcoding of several medicinal species in Gentiana from Yunnan province / 中国中药杂志

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.

Molecular structure and phylogenetic analyses of the complete chloroplast genomes of three original species of Pyrrosiae Folium / 中国天然药物

Pyrrosia petiolosa, Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium (PF) and commonly used as Chinese herbal medicines. Due to the similar morphological features of PF and its adulterants, common DNA barcodes cannot accurately distinguish PF species. Knowledge of the chloroplast (cp) genome is widely used in species identification, molecular marker and phylogenetic analyses. Herein, we determined the complete cp genomes of three original species of PF via high-throughput sequencing technologies. The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158 165 to 163 026 bp. The cp genomes of P. petiolosa and P. lingua encoded 130 genes, whilst that of P. sheareri encoded 131 genes. The complete cp genomes were compared, and five highly divergent regions of petA-psbJ, matK-rps16, ndhC-trnM, psbM-petN and psaC-ndhE were screened as potential DNA barcodes for identification of Pyrrosia genus species. The phylogenetic tree we obtained indicated that P. petiolosa and P. lingua are clustered in a single clade and, thus, share a close relationship. This study provides invaluable information for further studies on the species identification, taxonomy and phylogeny of Pyrrosia genus species.

Analysis on structure and phylogeny of complete chloroplast genomes in Psammosilene tunicoides / 中草药

Objective: To obtain the structural characteristics of chloroplast genome in Psammosilene tunicoides and analyze its phylogenetic position within the family of Caryophyllaceae. Methods: High-through-put sequencing technology and bioinformatic analysis softwares were used to analyze the structures of complete chloroplast genome of P. tunicoides. RAxML 8.2.11 software was utilized to reconstruct the Caryophyllaceae phylogentic tree with Amaranthus hypochondriacus as outgroup. Results: The complete chloroplast genome was 153 977 base pairs (bp) in size, including two inverted repeat (IR, 26 033 bp) regions separated by one large singe copy region (LSC, 84 385 bp) and one small singe copy region (SSC, 17 526 bp). The genome encoded 125 genes, of which 109 were unique, including 75 protein-coding genes (PCGs), 30 tRNA genes and 4 rRNA genes. The overall GC content of P. tunicoides was 36.5%, while those of IR regions (42.4%) were higher than LSC (34.2%) and SSC (30.1%) regions. The phylogenetic tree showed that P. tunicoides and Dianthus longicalyx were sister groups with 100% bootstrap value. All nodes of the phylogenetic tree of Caryophyllaceae were of high supports, and the ML tree had good resolution to reflect the phylogeny relationship among the Caryophyllaceae. Conclusion: The complete chloroplast genome of P. tunicoides and the phylogenetic relationship within Caryophyllaceae were analyzed in this study. The results will provide effective molecular information for further studies on evaluation of germplasm and molecular phylogeny of Caryophyllaceae.

High-throughput sequencing of complete chloroplast genome of Rheum tanguticum and its application in species identification / 中草药

Objective: To improve the survival status of wild Rheum tanguticum, which is threatened to meet the market demand, Illumina high-throughput sequencing technologies is used to bring new directions for relevant research. Methods The complete chloroplast genome of Rheum tanguticum was constructed with Illumina high-throughput sequencing technologies in this paper. Results: The genome was 161 054 bp in length, and exhibited a typical quadripartite structure of the large (LSC, 86 441 bp) and small (SSC, 12 745 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 30 934 bp each). The chloroplast genome contained 132 genes, including 88 protein-coding genes, 36 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes, 19 genes located in each IR area. Conclusion: The phylogenetic tree constructed with 11 sequences of seven Polygonaceae species and four other family species demonstrated a close relationship between R. tanguticum and R. palmatum in Polygonaceae, which was coincided with their morphological similarity, in addition, there were certain SNP sites in rpl32 and other genes, which provided a new basis for the effective identification of related species.

Complete chloroplast genome of Allium chinense: comparative genomic and phylogenetic analysis / 药学学报

italic>Allium chinense belongs to the genus Alliums of the lily family. It can be used both as medicine and food. To date, the phylogenetic relationship of Allium species have not be resolved completely. Furthermore, there has been a lack of DNA barcode to distinguish closely related species. In this study, the complete chloroplast genome of A. chinense was obtained using next generation DNA sequencing and bioinformatic analysis, and compared with that from other Allium species. The genome is a circular molecule of 152 525 bp with a typical quadripartite structure. Genome annotation identified a total of 116 genes, including 81 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Analyses of sequences from six Allium species showed that the most diverse regions are found in the protein coding regions such as ndhA and ycf1 genes, and in the intergenic regions, such as ps16-trnQ, trnT-trnF, ndhF-rpl32, rpl32-trnL and rpl16-rps3. A phylogenetic tree was constructed using 58 protein coding sequences from 53 species. All branches showed strong support with bootstrap scores reaching 66%-100%, except those for the Lilium and Paris. Our results suggest that the completed chloroplast genome could solve the classification problems of these species. Using EcoPrimer software, we identified seven markers from the chloroplast genomes, which can be used to differentiate congeneric species. In summary, we have sequenced the complete chloroplast genome of A. chinense, carried out phylogenetic analysis and identified a series of genus specific DNA barcode sequences. The results have laid the foundation for the systematical determination of the phylogenetic relationship of Allium species and the differentiation of species using the genus specific primers.