Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chestnut galls and leaf fungal communities

ABSTRACT: Fungal endophyte communities of Asian chestnut galls and surrounding leaf tissues

PROVIDER: PRJEB30131 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2984480.fastq.gz	Fastqsanger.gz
	ERR2984490.fastq.gz	Fastqsanger.gz
	ERR2984500.fastq.gz	Fastqsanger.gz
	ERR2984510.fastq.gz	Fastqsanger.gz
	ERR2984520.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 188

Similar Datasets

Transcriptome of mature Arabidopsis thaliana crown galls

2009-11-19 | GSE13927 | GEO

Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities.

Project description:Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.

| S-EPMC8801177 | biostudies-literature

Bark-inhabiting fungal communities of European chestnut undergo substantial alteration by canker formation following chestnut blight infection.

Project description:BackgroundChestnut forests are severely threatened by chestnut blight caused by the fungal pathogen Cryphonectria parasitica and the infected trees exhibit bark canker in the later stage of the disease. European chestnut (Castanea sativa) is further infected by Gnomoniopsis smithogilvyi, another canker-causing fungal pathogen. We explored whether and how chestnut blight is reflected in bark-inhabiting fungal communities of European chestnut and also assessed the co-occurrence of C. parasitica and G. smithogilvyi.Materials and methodsWe initially investigated the fungal communities of European chestnut bark tissues and further monitored changes in these fungal communities with regard to disease progression from infection to canker formation by analyzing bark samples from asymptomatic trees, asymptomatic trees with latent C. parasitica infection, and infected trees with canker tissues, using amplicon sequencing of the ITS2 region of rDNA.ResultsThe results showed that fungal community composition and diversity differed between the sample types. The fungal community composition was substantially reshaped by canker formation, whereas latent C. parasitica infection and more specifically pre-canker infection period per se had a weak effect. Fungal communities of canker samples was less diverse and more dissimilar to those of other sample types. C. parasitica dominated the mycobiome of canker samples, whereas G. smithogilvyi was found in only 9% of canker samples at very low abundances. However, G. smithogilvyi was a dominant fungus in the bark of healthy plants.ConclusionThis study highlights that canker formation is the principal driver of decreasing diversity and altered composition of the mycobiome in bark tissues of European chestnut infected by C. parasitica infection. It additionally emphasizes the scarce co-occurrence of C. parasitica and G. smithogilvyi on European chestnut.

| S-EPMC9911167 | biostudies-literature

Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica

Project description:Root-knot nematodes (RKNs) induce inside the vascular cylinder the giant cells (GCs) imbibed into a gall. Gene-repression in early developing GCs could be facilitated by small RNAs (sRNA) as miRNAs. 24nt-sRNAs, rasiRNAs and 21-22nt-sRNAs can also mediate epigenetic mechanisms. Three sRNA libraries from 3dpi galls and three from uninfected root segments were sequenced following Illumina-Solexa technology. Three sRNA libraries from 3dpi galls and three from uninfected root segments were sequenced

2015-11-19 | E-GEOD-71563 | biostudies-arrayexpress

Metrosideros galls

Project description:The transcriptional landscape of insect galls: psyllid (Hemiptera) gall formation in Hawaiian Metrosideros polymorpha (Myrtaceae)

| PRJEB11301 | ENA

Comparative transcriptome reprogramming in oak galls containing sexual or asexual generations of parasitoid wasps

Project description:Oak galls form when gall wasps lay their eggs into part of the tree; in some galls, this attachment point to the host consists of only a few cells. The gall itself comprises entirely of host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. This raises the intriguing question of the molecular mechanisms underlying gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path. Gall wasps undergo two generations each year, and the galls formed by these two generations exhibit markedly different appearances. We sequenced the transcriptomes of both the sexual and asexual generations of Neuropterus quercusbaccarum and Neuroterus numismalis. The transcriptomes of the generations that occur at the same time of year are more similar to each other than they are to the opposite generation of their respective species.

2024-06-18 | GSE244168 | GEO

Transcription profiling of Arabidopsis thaliana mature crown galls

Project description:This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age. Experiment Overall Design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately inoculated with Agrobacterium tumefaciens, strain C58, or mock-inoculated. Plants were cultivated for another 35 days under short day conditions (8 h illumination, 16 h darkness). Gene expression values of four independent experiments of treated material (C58 35dpi 1 to 4) were compared with four non-treated samples of the same age (reference 35dpi 1 to 4). Differential gene expression was analyzed by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).

2009-12-02 | E-GEOD-13927 | biostudies-arrayexpress

American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima)

Project description:American and Chinese chestnut cultivars genome sequencing and assembly

| PRJNA1147634 | ENA

Methylome of galls formed by Meloidogyne javanica in Arabidopsis thaliana at 14 days post infection

Project description:The goal of this study is to compare the methylation state of galls formed in Arabidopsis roots infected by Meloidogyne javanica at 14 days post infection compared to uninfected root segments (RC).

2022-07-31 | GSE156025 | GEO

Methylome of galls formed by Meloidogyne javanica in Arabidopsis thaliana at 3 days post infection

Project description:The goal of this study is to compare the methylation state of galls formed in Arabidopsis roots infected by Meloidogyne javanica at 3 days post infection compared to uninfected root segments (RC).

2022-07-31 | GSE155853 | 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