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The Ancient Evolutionary History of Polyomaviruses.

Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A - PLoS Pathog. (2016)

Bottom Line: To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods.Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages.The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

View Article: PubMed Central - PubMed

Affiliation: Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America.

ABSTRACT
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

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Related in: MedlinePlus

Midpoint-rooted phylogenetic tree for polyomavirus Large T antigen (LT) protein sequences.Species with different clade affiliations in VP1 analyses (Fig 4) are indicated in colored bold oblique text. The script ƒ character indicates fragmentary (sub-genomic) sequences. A key to species nicknames, genetic characteristics, and accession numbers is provided in S1 File. Percent bootstrap values are indicated for selected nodes. A FigTree file containing detailed bootstrap values is provided as S2 File. Scale bar shows one substitution per site.
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ppat.1005574.g003: Midpoint-rooted phylogenetic tree for polyomavirus Large T antigen (LT) protein sequences.Species with different clade affiliations in VP1 analyses (Fig 4) are indicated in colored bold oblique text. The script ƒ character indicates fragmentary (sub-genomic) sequences. A key to species nicknames, genetic characteristics, and accession numbers is provided in S1 File. Percent bootstrap values are indicated for selected nodes. A FigTree file containing detailed bootstrap values is provided as S2 File. Scale bar shows one substitution per site.

Mentions: Phylogenetic analysis of LT proteins (Fig 3) shows distinct clades corresponding to fish- and arthropod-associated sequences, as well as the previously recognized mammalian Ortho and Almi clades [27, 28]. Avian and bandicoot LT sequences together occupy a distinct clade. The appearance of the bandicoot virus LT protein sequences within this clade suggests that polyomaviruses with Avi-like early regions may infect modern marsupials. The avian and bandicoot LT proteins occupy a larger super-clade that loosely includes the newly identified fish-associated LT sequences. The LT protein sequences of the fish-associated polyomaviruses form a distinct clade that includes JEECV LT.


The Ancient Evolutionary History of Polyomaviruses.

Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A - PLoS Pathog. (2016)

Midpoint-rooted phylogenetic tree for polyomavirus Large T antigen (LT) protein sequences.Species with different clade affiliations in VP1 analyses (Fig 4) are indicated in colored bold oblique text. The script ƒ character indicates fragmentary (sub-genomic) sequences. A key to species nicknames, genetic characteristics, and accession numbers is provided in S1 File. Percent bootstrap values are indicated for selected nodes. A FigTree file containing detailed bootstrap values is provided as S2 File. Scale bar shows one substitution per site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836724&req=5

ppat.1005574.g003: Midpoint-rooted phylogenetic tree for polyomavirus Large T antigen (LT) protein sequences.Species with different clade affiliations in VP1 analyses (Fig 4) are indicated in colored bold oblique text. The script ƒ character indicates fragmentary (sub-genomic) sequences. A key to species nicknames, genetic characteristics, and accession numbers is provided in S1 File. Percent bootstrap values are indicated for selected nodes. A FigTree file containing detailed bootstrap values is provided as S2 File. Scale bar shows one substitution per site.
Mentions: Phylogenetic analysis of LT proteins (Fig 3) shows distinct clades corresponding to fish- and arthropod-associated sequences, as well as the previously recognized mammalian Ortho and Almi clades [27, 28]. Avian and bandicoot LT sequences together occupy a distinct clade. The appearance of the bandicoot virus LT protein sequences within this clade suggests that polyomaviruses with Avi-like early regions may infect modern marsupials. The avian and bandicoot LT proteins occupy a larger super-clade that loosely includes the newly identified fish-associated LT sequences. The LT protein sequences of the fish-associated polyomaviruses form a distinct clade that includes JEECV LT.

Bottom Line: To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods.Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages.The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

View Article: PubMed Central - PubMed

Affiliation: Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America.

ABSTRACT
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

Show MeSH
Related in: MedlinePlus