Rhizosphere metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA381669 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to research the ginseng leaf-stem gene expression profiles of and dig out its function genes in the leaf-expansion period, the transcriptomic sequencing technology was set up the first time for five years the transcription of the Panax ginseng leaf-stem in the leaf-expansion period.
2012-07-31 | E-MTAB-937 | biostudies-arrayexpress
Project description:Korean ginseng (Panax ginseng Meyer) has long been cultivated as an important medicinal plant. Drought results from the moderate water loss, which primarily impairs the growth of ginseng and reduction of yield loss. However, basis of biological clues to understanding the accurate mechanisms related to drought stress in proteome level are still elusive. Therefore, we carried out label-free quantitative proteomic analysis using ginseng roots subjected to drought stress which was grown at less than 10% soil moisture for two weeks, compared with normal ginseng which was grown at 25% soil moisture. The acquired proteins were carried out label-free proteomic analysis using LC-MS/MS. This approach led to the identification of total 2,471 proteins, and out of 195 proteins showed significant modulation. Functional classification revealed that proteins related to secondary metabolites, calcium signaling, and photosynthesis were enriched in control sample (cluster_1), while proteins associated with stress responsive, redox, electron transport, and protein synthesis were mainly dominated in cluster_2 (drought stress condition). Taken together, our results provided an overview of the drought-induced proteomic changes in ginseng root, and it is correlated with physiological changes, contributing to reveal potential marker at proteome level in ginseng.
2023-09-21 | PXD028602 | Pride
Project description:ginseng rhizospheric soil Raw sequence reads
| PRJNA397343 | ENA
Project description:Panax ginseng C.A. Meyer is one of the most popular medicinal herbs. In order to research the genes that related to the flowering period of ginseng, and find out the antifungal proteins and transcription factors that combat various biotic and abiotic stress, a cDNA sample was prepared from the flowering period ginseng root of a five-year-old plant and sequenced using the Illumina sequencing platform. In this study, we produced nearly 40 million sequencing reads. These reads were assembled into 134,045 contigs using Trinity software (mean size: 282 bp). Based on a similarity search with known proteins, we identified 79,307 sequences with a cut-off E-value of 10-5. Assembled sequences were then annotated using gene ontology (GO) terms, clusters of orthologous group (COG) classifications and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways respectively.
2014-07-25 | E-MTAB-1239 | biostudies-arrayexpress
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
2020-03-06 | GSE146427 | GEO