Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Batrachochytrium dendrobatidis

ABSTRACT: In vivo Bd gene expression

PROVIDER: PRJNA299101 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2719581.fastq.gz	Fastqsanger.gz
	SRR2719582.fastq.gz	Fastqsanger.gz
	SRR2719583.fastq.gz	Fastqsanger.gz
	SRR2719455.fastq.gz	Fastqsanger.gz
	SRR2723982.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Comparative genomics reveals intra and inter species variation in the pathogenic fungus Batrachochytrium dendrobatidis

Project description:The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.

2024-01-31 | GSE253912 | GEO

Batrachochytrium dendrobatidis

Project description:Complex History of the Bd Chytrid Fungus revealed through genome resequencing

| PRJNA183867 | ENA

Endogenized hypervirulence-associated DNA virus BdDV-1 is primarily restricted to enzootic lineages of the amphibian pathogen Batrachochytrium dendrobatidis

Project description:The Global Panzootic Lineage (GPL) of the pathogenic fungus Batrachochytrium dendrobatidis (Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly available Bd genome sequences, we identified multiple non-GPL Bd isolates that contain a circular Rep-encoding single stranded DNA-like virus which we named BdDV-1. We further sequenced and constructed genome assemblies with long read sequences to find that the virus is integrated into the nuclear genome in some strains. Attempts to cure virus positive isolates were unsuccessful, however, phenotypic differences between naturally virus positive and virus negative Bd isolates suggested that BdDV-1 decreases the growth of its host in vitro but increases the virulence of its host in vivo. BdDV-1 is the first described CRESS DNA mycovirus associated with hypervirulence with a distribution inversely associated with the emergence of the panzootic lineage.

2023-11-05 | GSE246809 | GEO

Common frog (Rana temporaria) transcriptomes following Exposure to Ranavirus and Batrachochytrium dendrobatidis

Project description:This experiment examined the transcriptional response of juvenile amphibian hosts (common frog, Rana temporaria) to two important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus. Common frogs are non-model organisms which do not have a reference genome.

2015-07-10 | E-MTAB-3632 | biostudies-arrayexpress

Transcription profiling of Xenopus tropicalis in response to infection by the chytrid Batrachochytrium dendrobatidis

Project description:Chytridiomycosis is an emerging infectious disease of amphibians caused by the chytrid Batrachochytrium dendrobatidis (Bd). The disease has been associated with global amphibian declines and is driving the species in the wild to extinction. Using DNA microarray technology we have analysed transcriptional changes in Xenopus tropicalis during the course (7 and 42 days) of infection by Bd under warm (26oC) and cold (18oC) temperatures.

2009-10-22 | E-MEXP-1936 | biostudies-arrayexpress

Batrachochytrium dendrobatidis

Project description:Chytrid fungus that caused the recent declines of global amphibian populations

| PRJNA13638 | ENA

Batrachochytrium dendrobatidis

Project description:The spatial epidemiology and molecular evolution of panzootic amphibian chytridiomycosis

| PRJNA413876 | ENA

Batrachochytrium dendrobatidis

Project description:DNAseq of Batrachochytrium dendrobatidis at BGI (Farrer et al PLoS Genet 2013)

| PRJNA174850 | ENA

Batrachochytrium dendrobatidis

Project description:DNAseq of Batrachochytrium dendrobatidis (Farrer et al PLoS Genet 2013)