Abstract
The scope for ecological studies of eukaryotic algal viruses has greatly improved with the development of molecular and bioinformatic approaches that do not require algal cultures. Here, we review the history and perceived future opportunities for research on eukaryotic algal viruses. We begin with a summary of the 65 eukaryotic algal viruses that are presently in culture collections, with emphasis on shared evolutionary traits (e.g., conserved core genes) of each known viral type. We then describe how core genes have been used to enable molecular detection of viruses in the environment, ranging from PCR-based amplification to community scale “-omics” approaches. Special attention is given to recent studies that have employed network-analyses of -omics data to predict virus-host relationships, from which a general bioinformatics pipeline is described for this type of approach. Finally, we conclude with acknowledgement of how the field of aquatic virology is adapting to these advances, and highlight the need to properly characterize new virus-host systems that may be isolated using preliminary molecular surveys. Researchers can approach this work using lessons learned from the Chlorella virus system, which is not only the best characterized algal-virus system, but is also responsible for much of the foundation in the field of aquatic virology.
Highlights
Viruses infecting eukaryotic algae are extremely diverse
Shotgun -omics further create the opportunity to identify virus-host pairs from environmental data and place them in semi-quantitative ecological context. These studies may even serve as preliminary assessments of the future cultivation requirements for isolating new virus-host systems. This burgeoning scientific frontier necessitates a review on the known diversity of eukaryotic algal viruses, the molecular toolkit available for in situ studies on their ecology, and the direction aquatic virology is taking to adapt to these methodologies
New virus isolates can be discovered from sequencing of single aquatic viruses sorted by flow cytometry, [169], as closely related, hyper diverse viruses are suggested to be difficult to assemble from metagenomes [170]
Summary
Viruses infecting eukaryotic algae are extremely diverse. They have been reported with DNA or RNA genomes in various architectures (linear, circular, double-stranded, single-stranded, segmented) and sizes (4.4 to 638kb) [1]. Electrophoretic gel [11]Network reprintedanalysis by permission. Shotgun -omics further create the opportunity to identify virus-host pairs from environmental data and place them in semi-quantitative ecological context These studies may even serve as preliminary assessments of the future cultivation requirements for isolating new virus-host systems. This burgeoning scientific frontier necessitates a review on the known diversity of eukaryotic algal viruses, the molecular toolkit available for in situ studies on their ecology, and the direction aquatic virology is taking to adapt to these methodologies
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