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ABSTRACT:
PROVIDER: PRJNA1310987 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The soldier fly is an endemic pest of sugarcane in Australia. Small numbers of larvae can cause significant damage to roots and reduce the crop yields. Little is known about the composition and function of the soldier fly salivary gland, its secretions, and their roles in insect-plant interactions. In this study, we performed transcriptome analysis of the salivary glands of starved and sugarcane root-fed soldier fly larvae. A total of 31,119 highly expressed assembled contigs were identified in the salivary glands and almost 50% of them showed high levels of similarity to known proteins in Nr databases. Of all the obtained contigs, only 9,727 sequences contain an open reading frame of over 100 amino acids. Around 31% of contigs were predicted to encode secretory proteins, including some digestive and detoxifying enzymes and potential effectors. Some known salivary secreted peptides such as serine protease, cysteine proteinase inhibitors, antimicrobial peptides and venom proteins were among the top 100 highly expressed genes. Differential gene expression analysis revealed significant modulation of 850 transcripts in salivary glands upon exposure to plant roots or starvation stress. Here, we identified some venom proteins which were significantly upregulated in the salivary glands of soldier fly larvae exposed to sugarcane roots. In other insects and nematodes some of these proteins have been used to manipulate host plant defense systems and facilitate the invasion of the host plant. These findings provide a further insight into the identification of potential effector proteins involved in soldier fly- sugarcane interactions.
2022-06-29 | GSE127658 | GEO
Project description:To explore the molecular mechanism of low-K tolerance in sugarcane, we have employed whole genome microarray expression profiling to identify sugarcane genes in response to low-K stress. seeldings were transplanted to low-K hydroponic (containing 0.1 mmol.L-1 K+) and the roots were collected at 0 (CK), 8, 24 and 72 h after exposure to low-K condition. The expressions of genes in sugarcane roots were detected by microarray analysis. Totally 1545 genes at 8 h, 1053 genes at 24 h and 3155 at 72 h differentially expressed under low-K stress, when the 2-fold change was adopted as the threshold for determining differentially expressed genes. Among these genes, a certain amount of transcription factors, transporters, kinases, oxidative stress-related genes and genes in Ca+ and ethylene signaling pathway were detected to differentially express. Seeldings were treated with low-K hydroponic (containing 0.1 mmol.L-1 K+) and after 0 (CK), 8, 24 and 72 h exposure to low -K stress, the roots of sugarcane were collected. Four independent experiments were performed using roots collected at different time points
2014-10-02 | E-GEOD-61935 | biostudies-arrayexpress
Project description:The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescens Pf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA aptamers with specificity for pyoverdine over other siderophores. Two DNA aptamers were isolated, and their features compared. The aptamers were applied to a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.
2024-07-18 | GSE225440 | GEO
Project description:Decrease in agricultural productivity in successive cuttings of sugarcane plants has been related to several extrinsic and intrinsic factors, even though no studies have been recently conducted to assess the physiological potential of sett roots in successive cuts in sugarcane culture. Proteomic studies on sugarcane sett roots at different cut stages are unknown. The UPLC-ESI-TOF-MS system and bioinformatics tools were used to identify proteins of sett roots in the first and fifth cuts of sugarcane cultivar RB966928 in the sprouting stage. The differences in proteome of sett roots from sugarcane cv. RB966928 in the first and fifth cut detected in current study support the hypothesis that the proteome of sett roots may change after successive cuts in sugarcane culture. A reduction in the number of proteins has been observed in the roots of the fifth cut, while 34% of proteins, identified exclusively in the first cut, were absent in the fifth one. Proteome analysis of sett roots in the first and fifth cut showed that the changes after successive cuts are not only quantitative, but mainly qualitative. The detailed list of proteins identified in the first cut but absent in the fifth cut reported in the present study is relevant since it opens a perspective for the lines of research that employ biotic or abiotic elicitors to induce gene expression for essential proteins absents in sett roots of the fifth cut, increasing the agricultural productivity and longevity of cane fields.
2021-12-14 | PXD023098 | JPOST Repository
Project description:To explore the molecular mechanism of low-K tolerance in sugarcane, we have employed whole genome microarray expression profiling to identify sugarcane genes in response to low-K stress. seeldings were transplanted to low-K hydroponic (containing 0.1 mmol.L-1 K+) and the roots were collected at 0 (CK), 8, 24 and 72 h after exposure to low-K condition. The expressions of genes in sugarcane roots were detected by microarray analysis. Totally 1545 genes at 8 h, 1053 genes at 24 h and 3155 at 72 h differentially expressed under low-K stress, when the 2-fold change was adopted as the threshold for determining differentially expressed genes. Among these genes, a certain amount of transcription factors, transporters, kinases, oxidative stress-related genes and genes in Ca+ and ethylene signaling pathway were detected to differentially express.
2014-10-02 | GSE61935 | GEO
Project description:Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h.
2013-11-21 | GSE42725 | GEO
Project description:A collection of 237,000 expressed sequence tags generated by the Sugarcane EST sequencing project (SUCEST) was analyzed in search of signal transduction components. The SUCAST (Sugarcane Signal Transduction) Catalogue contains over 3500 components, with around 2900 involved in several aspects of cell signaling and transcription. Sequence comparisons and conserved protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, a large number of small GTPases, G-proteins, members of the calcium and inositol metabolism, and other signal transduction-related proteins. Over 600 transcription factors were also indexed. Moreover, 437 genes with no matches in the public databases and 111 genes of unknown function were catalogued. Several of the SUCEST cDNA libraries were derived from plants submitted to abiotic stresses or infected with endophytic nitrogen fixing bacteria and stress and pathogen response-related genes were also annotated. The abundance of transcripts among six different sugarcane tissues (flowers, roots, leaves, lateral buds, 1st and 4th internodes) was evaluated using microarrays and expression profile clustering. We identified 216 genes that are significantly more abundant in one of the tissues analyzed. A subset of the data was validated by real-time PCR. Additionally, genes with similar expression levels among different tissues were identified. The characterization of these elements and their promoters can aid in the development of tools for the genetic manipulation of this plant species and other economically important grasses. Keywords: other
2005-08-24 | GSE1702 | GEO
Project description:We report raw bulk RNA sequencing data rice roots (X.kitaake) protoplasted for 2.5 hours and 3 hours to eliminate the effects of protoplasting duration on our scRNA-seq analysis, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions to verify our findsing with scRNA-seq studies
2024-12-08 | GSE283428 | GEO
Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.
2023-12-31 | GSE225299 | GEO
Project description:In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress.
2012-11-24 | GSE42483 | GEO