Plant metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA437068 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:Blue light perception by epiphytic Pseudomonas syringae drives chemoreceptor expression enabling efficient plant infection
2020-10-31 | GSE152188 | GEO
Project description:In this study we functionally characterized the grapevine VviNAC33 by its transient and stable overexpression in grapevine homologous system and the creation of its chimeric repressor. Through the application of DAP-seq approach we identified putative direct targets of VviNAC33, among which the SGR1 involved in the breakdown of chlorophyll. Stable VviNAC33 overexpressing transgenic plants displayed an obvious degreening effect on leaves and an inhibition of leaf growth. Consistently, transgenic plant expressing a chimeric repressor of the VviNAC33 showed the opposite phenotypic alterations. Our results evidenced that VviNAC33 is a direct player of leaf senescence program and propose a blueprint of the complex transcriptional regulatory network that govern organ phase transition in grapevine. transcription factor VviNAC33 is directly involved in leaf degreening and organ growth.
2021-07-07 | GSE155445 | GEO
Project description:The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. The shift to the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of neighboring genes and global regulation based on codon preference. A total of 54 grapevine samples, covering most of the Grape organs at different stages, were collected. Three biological replicates were taken for each sample, resulting in a total of 162 observations. The collected plant organs were: bud, inflorescence, tendril, leaf, stem, root, developing berry, withering berry, seed, rachis, anther, carpel, petal, pollen, and seedling.
2012-09-10 | E-GEOD-36128 | biostudies-arrayexpress
Project description:Epiphytic and planktonic bacteria diversity Targeted Locus (Loci)
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Project description:Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the US, vector transmission and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it was not possible to isolate or visualize viral particles from GRBV infected plants. Consequently, this has hampered the development of a serological assay that would facilitate GRBV detection in grapevine. We therefore decided to explore mass spectrometry approaches in order to quantify GRBV in infected plants and to identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in leaf petioles was determined to be in the range of 100 to 900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. The V1 copy number per unit wet tissue weight in leaves appeared to be about six times lower, and about 200-times lower in terms of protein concentration in the extractable protein mass than in petioles. We found a consistent upregulation of several enzymes involved in flavonoid biosynthesis in leaf and petiole extracts of GRBV-infected plants by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for grapevine leafroll associated virus infection on the transcriptome level. Last but not least, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting associated virus.
2018-12-19 | PXD011002 | Pride
Project description:Some insects can redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We addressed this possibility using RNA sequencing (RNAseq) to quantify the transcriptional responses of wild grapevine (Vitis riparia Michx.) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae (Fitch 1855)). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology classes were significantly enriched in developing galls, and that expression of many putative genes involved in flower formation was significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall, and perhaps other similar galls, appears to be phenotypically and transcriptionally convergent on the plant carpel.
2018-08-16 | GSE118569 | GEO