Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Global citrus root microbiome

PROVIDER: PRJNA844917 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19524000.fastq.gz	Fastqsanger.gz
	SRR19524001_1.fastq.gz	Fastqsanger.gz
	SRR19524001_2.fastq.gz	Fastqsanger.gz
	SRR19524002_1.fastq.gz	Fastqsanger.gz
	SRR19524002_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 86

Similar Datasets

Illumina miRNA sequencing revealed Citrus adaptation to long-term B-toxicity through modulation of lateral root development by miR319

Project description:We report the application of Illumina sequencing for high-throughput profiling of miRNA in citrus root responded to long-term boron toxicity. We find miR319 is involved in citrus adapation to long-term boron toxicity via targeting a MYB gene, Ciclev10000756m.g.v1.0, which is homologus with several MYBs that modulate lateral root development in Arabidopsis.

2021-02-25 | GSE111128 | GEO

Deciphering the Bacterial Microbiome of Citrus Plants in Response to ‘Candidatus Liberibacter asiaticus’-Infection and Antibiotic Treatments

Project description:Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. A powerful oligonucleotide microarray of high-density 16S rRNA genes, the PhyloChip microarray, has been developed and effectively used to study bacterial diversity, especially from environmental samples. In this article, we aim to decipher the bacterial microbiome in HLB-affected citrus versus non-infected citrus as well as in citrus plants treated with ampicillin and gentamicin using PhyloChip-based metagenomics.

2013-05-09 | GSE46728 | GEO

MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing

Project description:Background: Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils. Citrus are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some Citrus orchards. For the first time, we investigated Mg-deficiency-responsive miRNAs in ‘Xuegan’ (Citrus sinensis) roots using Illumina sequencing in order to obtain some miRNAs presumably responsible for Citrus Mg-deficiency tolerance. Results: We obtained 101 (69) miRNAs with increased (decreased) expression from Mg-starved roots. Our results suggested that the adaptation of Citrus roots to Mg-deficiency was related to the several aspects: (a) inhibiting root respiration and related gene expression via inducing miR158 and miR2919; (b) enhancing antioxidant system by down-regulating related miRNAs (miR780, miR6190, miR1044, miR5261 and miR1151) and the adaptation to low-phosphorus (miR6190); (c) activating transport-related genes by altering the expression of miR6190, miR6485, miR1044, miR5029 and miR3437; (d) elevating protein ubiquitination due to decreased expression levels of miR1044, miR5261, miR1151 and miR5029; (e) maintaining root growth by regulating miR5261, miR6485 and miR158 expression; and (f) triggering DNA repair (transcription regulation) by regulating miR5176 and miR6485 (miR6028, miR6190, miR6485, miR5621, miR160 and miR7708) expression. Mg-deficiency-responsive miRNAs involved in root signal transduction also had functions in Citrus Mg-deficiency tolerance. Conclusions: We obtained several novel Mg-deficiency-responsive miRNAs (i.e., miR5261, miR158, miR6190, miR6485, miR1151 and miR1044) possibly contributing to Mg-deficiency tolerance. These results revealed some novel clues on the miRNA-mediated adaptation to nutrient deficiencies in higher plants.

2017-07-28 | GSE80713 | GEO

Comprehensive analysis of small RNAs reveals insight into the tolerance of Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) to alkaline stress

Project description:Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.

2019-03-18 | GSE115049 | GEO

Root iTRAQ protein profile analysis of two Citrus species differing in aluminum-tolerance in response to long-term aluminum-toxicity

Project description:After long-term aluminum treatment, thereafter, we investigated Citrus root protein profiles using isobaric tags for relative and absolute quantification (iTRAQ).

2017-10-26 | PXD002301 | Pride

Phosphorus-mediated alleviation of aluminum toxicity revealed by iTRAQ technique in Citrus grandis roots

Project description:Citrus grandis seedlings were irrigated with nutrient solutions containing two levels of aluminium (Al; 0 mM and 1.2 mM AlCl3•6H2O) and two levels of phosphorus (P; 0 μM and 200 μM KH2PO4) combinations for 18 weeks, respectively. The proteome profile of Citrus root submitted to different P-Al interactions were investigated by using isobaric tags for relative and absolute quantification (iTRAQ).

2019-11-13 | PXD012534 | Pride

A flavonoid-attracted Aeromonas spp enhances plant Na_H1 resistance without cry-for-help [Bacteria_RNA-seq]

Project description:Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant Na_H1 resistance.

2022-10-19 | GSE184873 | GEO

A flavonoid-attracted Aeromonas spp enhances plant drought resistance without cry-for-help [Plant_RNA-seq]

2022-10-19 | GSE184872 | GEO

Comprehensive analysis of transcriptomes reveals insight into the tolerance of Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) to alkaline stress

2019-03-18 | GSE115048 | GEO

Coordination between the microbiota and the root diffusion barriers is required for plant mineral nutrient homeostasis

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data