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Heterocapsa circularisquama

ABSTRACT: Heterocapsa circularisquama overview

PROVIDER: PRJNA558417 | ENA |

REPOSITORIES: ENA

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			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

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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.

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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.

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