ABSTRACT
We intend to study the structural characteristics of Lycopus europaeus Linn. chloroplast genome and compare the evolutionary relationship of species from Lamiaceae with similar medicinal effects. The total DNA of Lycopus europaeus was sequenced using the Illumina Hiseq 4000 Sequencing platform and was assembled using NOVOplasty software. And then we annotated and analyzed the genome using the CPGAVAS2 online tool. We constructed the phylogenetic tree using the Stellera chamaejasme and Potentilla chinensis as the outgroup. The whole length of Lycopus europaeus chloroplast genome was 152 085 bp. A total of 132 genes were annotated including 88 protein-coding genes, 8 rRNA genes and 36 tRNA genes. Among them, 8 protein-coding genes (ndhB, rps7, rps12, rps19, rpl2, rpl23, ycf2, ycf15), 7 tRNA coding genes (trnM-CAU, trnL CAA, trnN-GUU, trnE-UUC, trnV-GAC, trnA-UGC, trnR-ACG) and 4 rRNA coding genes (rrn16s, rrn23s, rrn4.5s, rrn5s) are located in the IR region. There are 13 protein coding genes [rps16, rps19 (×2), atpF, rpoC1, rpl2 (×2), petB, petD, rpl16, ndhB (×2), ndhA] each contains one intron, two protein-coding genes (ycf3, clpP) each contain two introns, and 8 tRNA coding genes each contain one intron. A total of 34 SSRs were detected in the chloroplast genome of Lycopus europaeus. Phylogenetic analysis revealed that two species in the Lycopus genus, four species in the Dracocephalum genus, Glechoma longituba, two species in the Mentha genus and Prunella vulgari, in total 10 species are most related. The complete genome sequence of Lycopus europaeus was obtained and analyzed, which clarified the evolutional relationship between the species of Lycopus europaeus and in the Lamiaceae family.
ABSTRACT
italic>Inula japonica, Inula hupehensis and Inula linaariifolia are all medicinal plants of Inula L. in the Compositae family, and Inula hupehensis is endemic to China. In order to compare their genomic sequence differences and provide scientific basis for their germplasm conservation and development, we obtained and analyzed the complete chloroplast genomes of these three species. Total DNAs were extracted from fresh leaves and subjected to next-generation DNA sequencing. NOVOPlasty was used to assemble the chloroplast genomes from the sequence reads. CPGAVAS2 was used to annotate the genes and repeats in each genome. Lastly, phylogenomics analysis was conducted using RAxML. The results showed that the total length of the chloroplast genome of Inula japonica, Inula hupehensis and Inula linaariifolia is 150 754, 150 909, and 150 812 bp respectively, each consisting of a large single copy region, a small single copy region and a pair of inverted repeat regions. In addition, the G/C content of all three chloroplast genomes was approximately 37.7% and each encoded 111 unique genes, including 79 protein-coding, 28 tRNA and 4 rRNA genes. Meanwhile, 32, 33, 34 simple repeat sequences, 18, 22, 18 tandem repeat sequences and 33, 37, 38 scattered repeat sequences were identified in three species. Phylogenomic analysis showed that all three species of Inula L. and Pluchea indica were clustered together, with the relationship between Inuleae and Senecioneae closer, suggesting that Inuleae may have originated from the Senecioneae, not the Cardueae. The data in this study not only enriches the chloroplast genome database of Inula L., but also lays the foundation for the future studies of species identification, phylogenetic relationships, evolution history and genetic diversity of Inula species.
ABSTRACT
Medicinal materials in China differ in quality by different ecological types. Our research group found that there were two ecotypes of domestic Panax quinquefolium L. according to the characteristics of ginsenosides, inside versus outside Shanhaiguan. The genetic and ecological mechanisms of quality variation of Panax quinquefolium L. is unknown. Based on the genetic-chemical-ecological strategy, transcriptome and HPLC technology were used for comprehensive correlation analyses of transcriptomic data, ginsenoside content and environmental climate ecological factors. The transcriptomic results showed that key genes of ginsenoside biosynthesis, such as HMGR, AS and FPS, were significantly down-regulated in the inside Shanhaiguan ecotype. HPLC results showed that the quality of outside Shanhaiguan ecotype Panax quinquefolium L. was higher than that of the inside ecotype, with the content of ginsenosides in outside Panax quinquefolium L. was higher than that of inside ecotype except Rb2. Correlation analyses revealed that content of Panax quinquefolium L. ginsenoside is positively related to the expression levels of ginsenoside biosynthesis key genes (MK, HMGS, HMGR, and AS), and negatively related to the expression of glycosyl transferase (GT). The content of ginsenosides is negative related with climate factors, such as temperature, sunshine, and is positively related with moisture in both ecological environments. This study has provided a new mechanistic insight into the quality variations of two ecotypes for Panax quinquefolium L. and established a scientific basis for studying the ecological factors for the quality of traditional Chinese medicine.
ABSTRACT
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.
ABSTRACT
In this study,transcriptomics technique was used to investigate the mechanism of action of Aconiti Lateralis Radix Praeparata on acute heart failure rats induced by propafenone hydrochloride.First,rats were randomly divided into normal group,model group and administration group(1.25,2.5,5 g·kg-1).A rat with acute heart failure was constructed by intravenous femoral administration of proparone hydrochloride.The changes of heart rate,+dp/dtmaxand-dp/dtmaxat 5,10,20,30 and 60 min were recorded.Then another group of rats were given the same drug delivery method.In another group of animals,serum TNF-α could be determined by ELISA with the same dosage method.High-throughput sequencing technology was used to detect all gene expression differences in cardiac tissue samples of rats with acute heart failure.Through functional annotation and enrichment analysis,gene expression signaling pathways of rats with acute heart failure and rats with post-administration heart failure were screened out.The results showed that heart rate and LV+dp/dtmaxand LV-dp/dtmaxwere significantly decreased in the model group(P<0.05),while heart rate and LV+dp/dtmax and LV-dp/dtmaxwere significantly increased in the drug group(P<0.05,P<0.01).Moreover,ANP,BNP and TNF-α in acute heart failure rats was significantly decreased in high-dose aconite decoction group(P<0.05).Transcriptomics analysis showed that the mechanism of action was mainly related to activation of PI3 K-AKT signaling pathway and Jak-STAT pathway.Compared with the model group,aconite decoction up-regulated the expression of phosphatidylinostol 3-kinase(PI3 K),lysophosphatidic acid(LAP3),Bcl-3 and STAT genes,and down-regulated the expression of integrin(ITGA),nuclear orphan receptor(Nur77) genes.It could be concluded that the mechanism of aconite in treating acute heart failure rats may be related to the regulation of the PI3 k-Akt/Jak-STAT pathway.
Subject(s)
Animals , Rats , Aconitum , Chemistry , Drugs, Chinese Herbal , Pharmacology , Heart , Heart Failure , Drug Therapy , Metabolism , Myocardium , Metabolism , Random Allocation , Signal Transduction , TranscriptomeABSTRACT
The first genetic linkage map of Salvia miltiorrhiza was constructed in 94 F1 individuals from an intraspecific cross by using simple sequence repeat (SSR), sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. A total of 93 marker loci in the linkage map, consisting of 53 SSR, 38 SRAP and 2 ISSR locus were made up of eight linkage groups, covered a total length of 400.1 cm with an average distance of 4.3 cm per marker. The length of linkage groups varied from 3.3 -132 cm and each of them included 2-23 markers, separately. The result will provide important basis for QTL mapping, map-based cloning and association studies for commercially important traits in S. miltiorrhiza.