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Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics
Published on: February 18, 2009
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Unveiling the RNA virosphere associated with marine microorganisms
Syun-Ichi Urayama1,2, Yoshihiro Takaki1,3,4, Shinro Nishi1,4
1Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
Molecular Ecology Resources
|September 27, 2018
Summary
Marine RNA virus diversity is vast and largely hidden within host cells. A new sequencing method reveals a significant, previously unassessed population of intracellular RNA viruses in seawater.
Area of Science:
- Marine virology
- Metagenomics
- RNA virus research
Background:
- Extracellular viral DNA particle research is advanced.
- Intracellular marine viruses are a major source of extracellular particles but poorly understood.
- Current viral metagenomics primarily studies extracellular viruses.
Purpose of the Study:
- To investigate the genetic diversity of intracellular marine RNA viruses.
- To assess the previously unknown marine RNA virus population within cell fractions.
- To highlight the importance of studying cell fractions for complete viral diversity assessment.
Main Methods:
- Development and application of a novel sequencing method: fragmented and primer ligated dsRNA sequencing (flds) version 2.
- Analysis of cell fractions from surface seawater.
- Detection and characterization of RNA viral contigs within host cells and extracellular particles.
Main Results:
- Considerable genetic diversity of marine RNA viruses identified in cell fractions.
- Detected RNA virus community includes sequences from over half of known positive-sense ssRNA and dsRNA virus families, plus novel lineages.
- More dsRNA viral contigs were found in host cells than in extracellular viral particles, indicating a large, unassessed intracellular population.
Conclusions:
- Intracellular marine RNA viruses represent a significant and largely uncharacterized component of marine viral diversity.
- Studying cell fractions is crucial for a comprehensive understanding of global viral diversity.
- The flds v2 method effectively reveals hidden viral populations missed by traditional viral metagenomics.
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