Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

Charon, J; Murray, S; Holmes, EC

Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

Charon, J Murray, S

Holmes, EC

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Publisher:: Oxford University Press (OUP)
Publication Type:: Journal Article
Citation:: Virus Evolution, 2021, 7, (2), pp. veab070
Issue Date:: 2021-09-14

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Field	Value	Language
dc.contributor.author	Charon, J
dc.contributor.author	Murray, S https://orcid.org/0000-0001-7096-1307
dc.contributor.author	Holmes, EC
dc.date.accessioned	2021-10-06T03:02:33Z
dc.date.available	2021-10-06T03:02:33Z
dc.date.issued	2021-09-14
dc.identifier.citation	Virus Evolution, 2021, 7, (2), pp. veab070
dc.identifier.issn	2057-1577
dc.identifier.issn	2057-1577
dc.identifier.uri	http://hdl.handle.net/10453/150862
dc.description.abstract	<jats:title>Abstract</jats:title> <jats:p>Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.</jats:p>
dc.language	en
dc.publisher	Oxford University Press (OUP)
dc.relation	University of Technology Sydney
dc.relation	http://purl.org/au-research/grants/arc/FT120100704
dc.relation.ispartof	Virus Evolution
dc.relation.isbasedon	10.1093/ve/veab070
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0603 Evolutionary Biology, 0605 Microbiology
dc.title	Revealing RNA virus diversity and evolution in unicellular algae transcriptomes
dc.type	Journal Article
utslib.citation.volume	7
utslib.for	0603 Evolutionary Biology
utslib.for	0605 Microbiology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	open_access	*
dc.date.updated	2021-10-06T03:02:28Z
pubs.issue	2
pubs.publication-status	Published
pubs.volume	7
utslib.citation.issue	2

Abstract:

Abstract Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.

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http://hdl.handle.net/10453/150862