Plant metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA360242 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Illumina HiSeq technology was used to generate mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) . Control roots or ectomycorrhizal root tips were harvested after 1 month and used for RNA extraction. Paired-end (2X150bp) reads were generated and aligned to Eucalyptus grandis transcripts (http://www.phytozome.net/; primarytranscripts only) using CLC Genomics Workbench 6.
2014-10-10 | GSE62227 | GEO
Project description:We conducted field surveys to detect the population density of the most important invasive weed species and their associated virus vectoring aphids in crops grown under high input (HIF) vs low-input (LIF) field conditions, with and without fertilizers and pesticides. The most frequent invasive weed species were Stenactis annua, Erigeron canadensis and Solidago canadensis. These species were hosts predominantly for the aphids Brachycaudus helichrysi and Aulacorthum solani in both management systems. The 13% higher coverage of S. annua under LIF conditions resulted in a 30% higher B. helichrysi abundance and ~85% higher A. solani abundance compared with HIF conditions. To reveal virus infection in crop plants and invasive weeds high-throughput sequencing of small RNAs were carried out. Bioinformatics analysis of the results detected the presence of 16 important plant viruses, but not resulting strikingly different pattern under LIF and HIF. This could suggest that invasive weeds serves as a virus reservoir both under low and high input management systems. The lake of any management increases virus vector aphids abundances, their presence has a great impact on the viromes of the crops.
2020-06-03 | GSE132755 | GEO
Project description:Comparison of bacterial community composition of soybean roots grown in different nitrogen conditions
| PRJDB11077 | ENA
Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.
2020-11-01 | GSE151376 | GEO
Project description:Real-time quantitative PCR (RT–qPCR) is the favoured method for gene expression analysis in molecular biology due to its sensitivity, specificity, cost-effectiveness, and reproducibility. To obtain the accuracy and reliability of RT-qPCR, the use of reliable reference genes is inevitable. There were many reports about the physiological response of giant reed (Arundo donax L.) to abiotic stresses. However, there is little use in the validation of reference genes under different treatments. It still belongs to the blank that the research about selecting reference genes under salt and alkali. In this study, the expression stability of twenty-three candidate reference genes in leaves and roots were assessed under salt, drought, and alkali stresses using geNorm, NormFinder, BestKeeper, and Delta Ct algorithms. Our results showed that no one gene had an invariant expression under different conditions. For example, under drought stress, UPL3, UBC2, and APT1 were better reference genes in leaves, RPL5 and FPS2 were better in roots. Under alkali stress, GAPDH, APT1, and RPS5 were better reference genes in leaves; UPL3, ACT2, and SAMDC2 were better in roots. In addition, the expression of MSD1 was used to further confirm the validated reference genes under salt, drought, and alkali stresses. It was proved that the use of inappropriate reference genes in giant reed significantly altered the relative expression of target genes and even reversed the results. Consequently, our results provided guidelines for reference gene selection under salt, drought, and alkali stresses and a foundation for more accurate and widespread use of RT-qPCR in the giant reed.
2021-12-15 | GSE190890 | GEO
Project description:metagenome from agricultural soil from Utah under different nitrogen management
| PRJNA510146 | ENA
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
Project description:Soil samples under different storage conditions Genome sequencing
| PRJNA258114 | ENA