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Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene.

Taylor DJ, Ballinger MJ, Zhan JJ, Hanzly LE, Bruenn JA - PeerJ (2014)

Bottom Line: For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial.Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses.Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, The State University of New York at Buffalo , Buffalo, NY , USA.

ABSTRACT
An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.

No MeSH data available.


Related in: MedlinePlus

DNA sequence validation of integration for the filoviral VP35-like sequence in voles of the genus Microtus.The section of the intron common to rodent introns is highlighted in gray and the proposed filovirid-like insert is highlighted in red. Sequence comparisons (colored blocks are differences) between the PCR product (black bar) for the meadow vole (M. pennsylvanicus) and the genome assembly for the prairie vole (M. ochrogaster) are shown for (A) the shared intron of rodent genomes and (B) the proposed insert containing a filovirid VP35-like sequence in genomes of cricetid rodents.
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fig-3: DNA sequence validation of integration for the filoviral VP35-like sequence in voles of the genus Microtus.The section of the intron common to rodent introns is highlighted in gray and the proposed filovirid-like insert is highlighted in red. Sequence comparisons (colored blocks are differences) between the PCR product (black bar) for the meadow vole (M. pennsylvanicus) and the genome assembly for the prairie vole (M. ochrogaster) are shown for (A) the shared intron of rodent genomes and (B) the proposed insert containing a filovirid VP35-like sequence in genomes of cricetid rodents.

Mentions: The occurrences are unlikely to be assembly artifacts because the genomes in question are NCBI reference genomes with strong sequence coverage. The striped dwarf hamster (C. griseus) has independent genome assemblies that agree on the insert locations. Also, the only mammalian species in this filovirid clade are cricetid rodents, some of which have identical insertion locations in their genomes. The pattern of shared insertion among monophyletic taxa is a prediction of common ancestry rather than of assembly artifacts. Finally, we carried out PCR in the meadow vole using primers designed to flank the VP35-like region of the prairie vole (which has a genome project). The PCR reaction was positive and the sequence had strong identity to the microtine sequence from the genome assembly (Fig. 3). Excluding indels the sequence across this putative insert region showed 94% (583 nt) identity between the genome assembly of the pairie vole (M. ochrogaster) and the PCR product of the meadow vole (M. pennsylvanicus). Our partial sequence is consistent with an orthologous insert of a VP35-like sequence in the genome of the meadow vole (M. pennsylvanicus) and confirms the assembled location of this region in rodents in the 3′ intron of the Tax1-binding protein 1 (TAX1BP1) gene locus.


Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene.

Taylor DJ, Ballinger MJ, Zhan JJ, Hanzly LE, Bruenn JA - PeerJ (2014)

DNA sequence validation of integration for the filoviral VP35-like sequence in voles of the genus Microtus.The section of the intron common to rodent introns is highlighted in gray and the proposed filovirid-like insert is highlighted in red. Sequence comparisons (colored blocks are differences) between the PCR product (black bar) for the meadow vole (M. pennsylvanicus) and the genome assembly for the prairie vole (M. ochrogaster) are shown for (A) the shared intron of rodent genomes and (B) the proposed insert containing a filovirid VP35-like sequence in genomes of cricetid rodents.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4157239&req=5

fig-3: DNA sequence validation of integration for the filoviral VP35-like sequence in voles of the genus Microtus.The section of the intron common to rodent introns is highlighted in gray and the proposed filovirid-like insert is highlighted in red. Sequence comparisons (colored blocks are differences) between the PCR product (black bar) for the meadow vole (M. pennsylvanicus) and the genome assembly for the prairie vole (M. ochrogaster) are shown for (A) the shared intron of rodent genomes and (B) the proposed insert containing a filovirid VP35-like sequence in genomes of cricetid rodents.
Mentions: The occurrences are unlikely to be assembly artifacts because the genomes in question are NCBI reference genomes with strong sequence coverage. The striped dwarf hamster (C. griseus) has independent genome assemblies that agree on the insert locations. Also, the only mammalian species in this filovirid clade are cricetid rodents, some of which have identical insertion locations in their genomes. The pattern of shared insertion among monophyletic taxa is a prediction of common ancestry rather than of assembly artifacts. Finally, we carried out PCR in the meadow vole using primers designed to flank the VP35-like region of the prairie vole (which has a genome project). The PCR reaction was positive and the sequence had strong identity to the microtine sequence from the genome assembly (Fig. 3). Excluding indels the sequence across this putative insert region showed 94% (583 nt) identity between the genome assembly of the pairie vole (M. ochrogaster) and the PCR product of the meadow vole (M. pennsylvanicus). Our partial sequence is consistent with an orthologous insert of a VP35-like sequence in the genome of the meadow vole (M. pennsylvanicus) and confirms the assembled location of this region in rodents in the 3′ intron of the Tax1-binding protein 1 (TAX1BP1) gene locus.

Bottom Line: For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial.Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses.Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, The State University of New York at Buffalo , Buffalo, NY , USA.

ABSTRACT
An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.

No MeSH data available.


Related in: MedlinePlus