Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1053841 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27238657_1.fastq.gz | Fastqsanger.gz | |||
| SRR27238657_2.fastq.gz | Fastqsanger.gz | |||
| SRR27238658_1.fastq.gz | Fastqsanger.gz | |||
| SRR27238658_2.fastq.gz | Fastqsanger.gz | |||
| SRR27238659_1.fastq.gz | Fastqsanger.gz |
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Project description:Radix bupleuri is a traditional Chinese crude drug and it is still widely used in contemporary medicine. Bupleurum chinense DC. and B. scorzonerifolium Willd. are officially recorded as the source species of Radix bupleuri in Pharmacopoeia of the PeopleM-bM-^@M-^Ys Republic of China. The obvious difference in chemical active components and pharmacological action of Radix bupleuri derived from the two species has caused attention. But to date, no definite criterions and regulates are issued based on plant species sources to direct the standard uses of Radix bupleuri for their extracts and traditional decoction pieces in medical market. Using 454-FLX pyrosequencing with one half-plate run for each cDNA library, a total of 419,576 and 416,112 reads, among those 313,483 and 342,263 high quality ESTs were obtained for B. chinense and B. scorzonerifolium, respectively. The average read length was 279 bp and 310 bp, respectively. The assembled 28,897 and 30,912 unigenes for B. chinense and B. scorzonerifolium were successively annotated based on sequence similarity by major public nucleotide/protein databases, Nt, Nr, SwissProt, KEGG, COG, Interpro and GO. Based on the alignments, 71.9% (20,787) and 75.8% (23,426) of the total unigenes for B. chinense and B. scorzonerifolium could be matched to nucleotides from NCBI Nt database. Certain percent from 27.1% (7,820) to 70.8% (20,461) of the total unigenes for B. chinense, and from 26.4% (8,145) to 72.1% (22,289) of the total unigenes for B. scorzonerifolium, could be matched to proteins from different databases. For the same database, similar percent of the total unigenes for B. chinense and B. scorzonerifolium were annotated. A total of 17,117 (59.2%) and 19,416 (62.8%) unigenes for B. chinense and B. scorzonerifolium could be found homologous genes in opposite dataset. According to KEGG annotation, 3,637 and 3,821 unigenes were assigned relating to metabolism in datasets of B. chinense and B. scorzonerifolium, respectively. Carbohydrate metabolism, energy metabolism and amino acid metabolism were the highest three groups in metabolism category and followed by lipid metabolism group for B. chinense. In comparison, lipid metabolism group had most unigenes for B. scorzonerifolium and it had much more unigenes than the same group for B. chinense (827 to 562). A total of 70 and 52 unigenes were related to metabolism of terpenoids and polyketides in two separate datasets, which seems agree with the situation of higher content of terpenoid saikosaponins in B. chinense than B. scorzonerifolium in some extent. To compare the biosynthesis of main bioactive components in roots of B. chinense and B. scorzonerifolium, putative genes which may participate in the biosynthesis of terpenoid, triterpenoid, sterol, ligan and flavonoid were searched according to unigenes annotation. Most lignan and flavonoid biosynthesis related genes were found in both datasets of B. chinense and B. scorzonerifolium, while some terpenoid or triterpenoid related genes were dominantly found in the dataset of B. chinense. This reflected in some extent that these genes expressed in low levels and relative metabolites were biosynthesized in lower quantities in roots of B. chinense than those of B. scorzonerifolium. Besides abovementioned comparison on two transcriptome, the expression of some genes involved in biosyntheses of main medicinal secondary metabolites were analyzed by qRT-PCR in roots of the two species. These molecular biological data will make a useful clue and arouse more studies on the reasonable application of the two Bupleurum species. The fine roots of two-year old plants of B. chinense and B. scorzonerifolium planted in the same place at the same time were collected at the usual harvest time of medicinal materials of Bupleurum. Those roots from the two species plants were used for 454 sequencing.
2013-09-27 | E-GEOD-51187 | biostudies-arrayexpress
Project description:Radix bupleuri is a traditional Chinese crude drug and it is still widely used in contemporary medicine. Bupleurum chinense DC. and B. scorzonerifolium Willd. are officially recorded as the source species of Radix bupleuri in Pharmacopoeia of the People’s Republic of China. The obvious difference in chemical active components and pharmacological action of Radix bupleuri derived from the two species has caused attention. But to date, no definite criterions and regulates are issued based on plant species sources to direct the standard uses of Radix bupleuri for their extracts and traditional decoction pieces in medical market. Using 454-FLX pyrosequencing with one half-plate run for each cDNA library, a total of 419,576 and 416,112 reads, among those 313,483 and 342,263 high quality ESTs were obtained for B. chinense and B. scorzonerifolium, respectively. The average read length was 279 bp and 310 bp, respectively. The assembled 28,897 and 30,912 unigenes for B. chinense and B. scorzonerifolium were successively annotated based on sequence similarity by major public nucleotide/protein databases, Nt, Nr, SwissProt, KEGG, COG, Interpro and GO. Based on the alignments, 71.9% (20,787) and 75.8% (23,426) of the total unigenes for B. chinense and B. scorzonerifolium could be matched to nucleotides from NCBI Nt database. Certain percent from 27.1% (7,820) to 70.8% (20,461) of the total unigenes for B. chinense, and from 26.4% (8,145) to 72.1% (22,289) of the total unigenes for B. scorzonerifolium, could be matched to proteins from different databases. For the same database, similar percent of the total unigenes for B. chinense and B. scorzonerifolium were annotated. A total of 17,117 (59.2%) and 19,416 (62.8%) unigenes for B. chinense and B. scorzonerifolium could be found homologous genes in opposite dataset. According to KEGG annotation, 3,637 and 3,821 unigenes were assigned relating to metabolism in datasets of B. chinense and B. scorzonerifolium, respectively. Carbohydrate metabolism, energy metabolism and amino acid metabolism were the highest three groups in metabolism category and followed by lipid metabolism group for B. chinense. In comparison, lipid metabolism group had most unigenes for B. scorzonerifolium and it had much more unigenes than the same group for B. chinense (827 to 562). A total of 70 and 52 unigenes were related to metabolism of terpenoids and polyketides in two separate datasets, which seems agree with the situation of higher content of terpenoid saikosaponins in B. chinense than B. scorzonerifolium in some extent. To compare the biosynthesis of main bioactive components in roots of B. chinense and B. scorzonerifolium, putative genes which may participate in the biosynthesis of terpenoid, triterpenoid, sterol, ligan and flavonoid were searched according to unigenes annotation. Most lignan and flavonoid biosynthesis related genes were found in both datasets of B. chinense and B. scorzonerifolium, while some terpenoid or triterpenoid related genes were dominantly found in the dataset of B. chinense. This reflected in some extent that these genes expressed in low levels and relative metabolites were biosynthesized in lower quantities in roots of B. chinense than those of B. scorzonerifolium. Besides abovementioned comparison on two transcriptome, the expression of some genes involved in biosyntheses of main medicinal secondary metabolites were analyzed by qRT-PCR in roots of the two species. These molecular biological data will make a useful clue and arouse more studies on the reasonable application of the two Bupleurum species.
2013-09-27 | GSE51187 | GEO
Project description:Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing unprecedented changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in the Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
2012-06-01 | GSE33847 | GEO
Project description:Transcriptome sequencing of Bupleurum chinense and Bupleurum scorzonerifolium
| PRJNA852406 | ENA
Project description:Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.
2021-07-12 | GSE179671 | GEO