Kim Stevens

Abstract

Brown algae are important primary producers and habitat formers in coastal environments and are believed to have evolved multicellularity independently of the other eukaryotes. The phaeoviruses that infect them form a stable lysogenic relationship with their host via genome integration, but have only been extensively studied in two genera: Ectocarpus and Feldmannia. In this study I aim to improve our understanding of the genetic diversity, host range and distribution of phaeoviruses. Sequencing and phylogenetic analysis of amplified fragments of three core phaeoviral genes (encoding major capsid protein (MCP), DNA polymerase and superfamily III helicase) of phaeovirus infected algae confirmed the suspected phaeoviral identity of viruses infecting E. fasciculatus, F. simplex, Pilayella littoralis, Myriotrichia clavaeformis and Hincksia hincksiae. Furthermore, this approach revealed multiple virus sequence variants within individual strains, and moreover that the variants formed two distinct subgroups. Subgroup A was highly conserved and observed in multiple algal genera, whereas subgroup B was much more diverse, but only found in Feldmannia species. Transcriptome sequencing of an actively infected F. irregularis strain revealed polymorphisms within key viral genes, suggesting that multiple variants were indeed active within this strain. High resolution melt curve (HRM) technology was used to develop a high throughput screening method for detecting phaeoviral MCP as a proxy for detection of phaeoviruses. This technique was also able to assign 88% of those detected to one of the subgroups, based on their differing melting temperature distributions. This was then applied to 1034 Ectocarpus isolates collected from around Europe and South America, and in accordance with previous studies of phaeoviral infection, 43-79% of strains contain virus sequence (depending on species). 17% of the isolates tested even contained sequence from both subgroups. 82 Laminariales strains, close relatives of the Ectocarpales, were also screened because they comprise commercially important kelp species but are not known to be infected by viruses. 10-17% of these tested positive for phaeoviral MCP, which when sequenced formed a separate group within the phaeoviruses. This finding could have a major impact on the kelp farming industry if the viruses are found to affect reproduction as happens in the Ectocarpales. The discovery of two subgroups is contrary to current beliefs that the phaeoviruses are a single monophyletic group, and that each species of alga has its own phaeovirus, casting doubt on the usefulness of the current convention of naming each phaeovirus after its host. It appears that the subgroup B viruses have begun to evolve away from the stable, K-selected subgroup A viruses towards a more r- type strategy with higher mutation and diversification. This study has identified potential mechanisms that may influence this shift, including mutations in a region of the DNA polymerase known to negatively affect DNA replication fidelity, combined with an active integrase and lack of a proofreading exonuclease, along with the observed infection of individuals with both phaeovirusal subgroups. The resulting mutations and recombinations could lead to the diversity observed here, and may provide a suitable model for the study of other emergent virus infections.

Keywords

Evolution, Diversity, Prevalence, Brown algae, NCLDV, Phaeovirus

Document Type

Thesis

Publication Date

2014

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