Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Heterocapsa circularisquama

ABSTRACT: Transcriptome of Heterocapsa circularisquama (mRNA-seq)

PROVIDER: PRJDB7513 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR186650_1.fastq.gz	Fastqsanger.gz
	DRR186650_2.fastq.gz	Fastqsanger.gz
	DRR186651_1.fastq.gz	Fastqsanger.gz
	DRR186651_2.fastq.gz	Fastqsanger.gz
	DRR186652_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Heterocapsa circularisquama

Project description:Heterocapsa circularisquama overview

| PRJNA558417 | ENA

Heterocapsa circularisquama strain:HU9433

Project description:Heterocapsa circularisquama strain:HU9433 Transcriptome or Gene expression

| PRJNA319447 | ENA

Heterocapsa circularisquama RNA virus 01 strain:A8

Project description:Genome sequencing of Heterocapsa circularisquama RNA virus strain A8

| PRJDB15509 | ENA

Heterocapsa niei

Project description:Heterocapsa niei Genome sequencing and assembly

| PRJNA827466 | ENA

Heterocapsa rotundata strain:HRSH1201

Project description:Heterocapsa rotundata strain:HRSH1201 Transcriptome or Gene expression

| PRJNA638785 | ENA

Comparison of genome sequences of single-stranded RNA viruses infecting the bivalve-killing dinoflagellate Heterocapsa circularisquama.

Project description:Heterocapsa circularisquama RNA virus (HcRNAV) has at least two ecotypes (types UA and CY) that have intraspecies host specificities which are complementary to each other. We determined the complete genomic RNA sequence of two typical HcRNAV strains, HcRNAV34 and HcRNAV109, one of each ecotype. The nucleotide sequences of the viruses were 97.0% similar, and each had two open reading frames (ORFs), ORF-1 coding for a putative polyprotein having protease and RNA-dependent RNA polymerase (RdRp) domains and ORF-2 encoding a single major capsid protein. Phylogenetic analysis of the RdRp amino acid sequence suggested that HcRNAV belongs to a new previously unrecognized virus group. Four regions in ORF-2 had amino acid substitutions when HcRNAV34 was compared to HcRNAV109. We used a reverse transcription-nested PCR system to amplify the corresponding regions and also examined RNAs purified from six other HcRNAV strains with known host ranges. We also looked at natural marine sediment samples. Phylogenetic dendrograms for the amplicons correlated with the intraspecies host specificities of the test virus strains. The cloned sequences found in sediment also exhibited considerable similarities to either the UA-type or CY-type sequence. The tertiary structure of the capsid proteins predicted using computer modeling indicated that many of the amino acid substitutions were located in regions on the outside of the viral capsid proteins. This strongly suggests that the intraspecies host specificity of HcRNAV is determined by nanostructures on the virus surface that may affect binding to suitable host cells. Our study shows that capsid alterations can change the phytoplankton-virus (host-parasite) interactions in marine systems.

| S-EPMC1317472 | biostudies-literature

High interaction variability of the bivalve-killing dinoflagellate Heterocapsa circularisquama strains and their single-stranded RNA virus HcRNAV isolates.

Project description:HcRNAV is a single-stranded RNA (ssRNA) virus that specifically infects the bivalve-killing dinoflagellate, Heterocapsa circularisquama. HcRNAV strains are grouped into 2 types (UA and CY), based on intra-species host specificity and the amino acid sequence of the major capsid protein (MCP). In the present study, we report the isolation of novel HcRNAV clones (n=51) lytic to the H. circularisquama strains, HU9433-P, HCLG-1, 05HC05 and 05HC06. HcRNAV34, HcRNAV109, HcRNAV641, and HcRNAV659, which displayed lytic activity against the strains, HU9433-P, HCLG-1, 05HC05, and 05HC06, respectively, were selected as typical virus clones and were intensively examined. The infection intensity of each host-virus combination was analyzed by examining the algicidal activity, detecting the intracellular replication of the viral RNA as well as the appearance of host cells with a morphologically abnormal nucleus post-infection. Interestingly, the strains, 05HC05 and 05HC06, were markedly sensitive to HcRNAV641 and HcRNAV659, respectively. Tertiary structural modeling predicted 4 unique amino acid (aa) substitutions in HcRNAV659-MCP to be exposed to an ambient water environment, which contributed towards determining its infection specificity. Neighbor-joining analysis of MCP aa sequences from HcRNAV clones revealed 3 clades, namely, the CY type and the UA1 and UA2 subtypes. The HcRNAV clones lytic to HCLG-1 (ex. HcRNAV109), HU9433-P and 05HC05 (ex. HcRNAV34), and 05HC06 (ex. HcRNAV659) were categorized into CY type, UA1 and UA2 subtypes, respectively. The present study highlights the complexity of the H. circularisquama-HcRNAV host-virus system, i.e., clonal variation, microbial control, and ecology in a natural algal population.

| S-EPMC4070693 | biostudies-literature

Heterocapsa circularisquama RNA virus 01

Project description:A PCR-based assay targeting the major capsid protein gene of a dinorna-like ssRNA virus that infects coral photosymbionts: Raw sequence reads

| PRJNA394026 | ENA

RNA-seq of dinoflagellate Heterocapsa sp. strain CCAP 1125/4

Project description:RNA-seq of dinoflagellate Heterocapsa sp. strain CCAP 1125/4

| PRJEB56598 | ENA

Current environmental status of the oyster farms on Lake Kamo in Japan; viral control of the harmful bloom of <i>Heterocapsa circularisquama</i>.

Project description:Lake Kamo is an enclosed, low-inflow estuary connected to the open sea that is famous for oyster farming in Japan. In the fall of 2009, this lake experienced its first bloom of the dinoflagellate Heterocapsa circularisquama, which selectively kills bivalve mollusks. This species has been detected exclusively in southwestern Japan. The completely unexpected outbreak of H. circularisquama in the northern region is believed to have been caused by the contamination of purchased seedlings with this species. The water quality and nutrient data collected by our group from July through October over the past 10 years revealed that the environment of Lake Kamo has not changed significantly. However, in the open water around Sado Island, where Lake Kamo is located, the water temperature has increased by 1.80 °C in the last 100 years, which is equivalent to 2-3-fold the world average. This has resulted in a rise in the sea level, which is expected to further deteriorate the water exchange between Lake Kamo and the open sea and low dissolved oxygen in the bottom layer of the Lake and the associated dissolution of nutrients from the bottom sediment. Therefore, seawater exchange has become insufficient and the lake has become nutrient rich, making it prone to the establishment of microorganisms, such as H. circularisquama, once they have been introduced. We developed a method to mitigate the damage caused by the bloom by spraying sediments containing the H. circularisquama RNA virus (HcRNAV), which infects H. circularisquama. After ∼10 years of performing various verification tests, including field trials, this method was used at the Lake in 2019. During the 2019 H. circularisquama growth season, a small amount of sediment containing HcRNAV was sprayed on the lake three times, which resulted in a decrease in H. circularisquama and an increase in HcRNAV, indicating that this method is effective in diminishing the bloom.

| S-EPMC10183167 | biostudies-literature

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