Limits...
A phylogenomic data-driven exploration of viral origins and evolution.

Nasir A, Caetano-Anollés G - Sci Adv (2015)

Bottom Line: Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data.Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the "viral supergroup" and the existence of widespread episodes of horizontal transfer of genetic information.Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA.

ABSTRACT
The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the "viral supergroup" and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts.

No MeSH data available.


Related in: MedlinePlus

Ancient history of RNA viral proteomes.(A) The length of Ariadne’s threads (colored lines) identifies FSFs that were shared by more than three viral subgroups. Filled circles indicate FSFs shared between two or three viral subgroups. Numbers next to each circle give the mean nd of FSFs shared by each combination. Numbers in parentheses give the range between the most ancient and the most recent FSFs that were shared by each combination. (B) Distribution of the most ancient (nd < 0.3) ABEV FSFs in evolutionary timeline (nd) for each viral subgroup. Numbers in parentheses indicate the total FSFs in each viral subgroup. White circles indicate group medians. A density trace is plotted symmetrically around the boxplots.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4643759&req=5

Figure 6: Ancient history of RNA viral proteomes.(A) The length of Ariadne’s threads (colored lines) identifies FSFs that were shared by more than three viral subgroups. Filled circles indicate FSFs shared between two or three viral subgroups. Numbers next to each circle give the mean nd of FSFs shared by each combination. Numbers in parentheses give the range between the most ancient and the most recent FSFs that were shared by each combination. (B) Distribution of the most ancient (nd < 0.3) ABEV FSFs in evolutionary timeline (nd) for each viral subgroup. Numbers in parentheses indicate the total FSFs in each viral subgroup. White circles indicate group medians. A density trace is plotted symmetrically around the boxplots.

Mentions: (ii) Ariadne’s threads traced in evolutionary time. We traced FSF domain ages onto the threads of FSFs shared between viral subgroups (Fig. 6A). The oldest domains were spread in a transect that unified minus-ssRNA, plus-ssRNA, and dsRNA proteomes. This pattern was clearly evident in violin plots that describe FSF age in the threads along the early timeline of domain evolution (nd < 0.3) (Fig. 6B). Once again, the proteomes of minus-ssRNA viruses were particularly enriched in ancient domains, suggesting that perhaps ssRNA was involved in virocell origins (read below).


A phylogenomic data-driven exploration of viral origins and evolution.

Nasir A, Caetano-Anollés G - Sci Adv (2015)

Ancient history of RNA viral proteomes.(A) The length of Ariadne’s threads (colored lines) identifies FSFs that were shared by more than three viral subgroups. Filled circles indicate FSFs shared between two or three viral subgroups. Numbers next to each circle give the mean nd of FSFs shared by each combination. Numbers in parentheses give the range between the most ancient and the most recent FSFs that were shared by each combination. (B) Distribution of the most ancient (nd < 0.3) ABEV FSFs in evolutionary timeline (nd) for each viral subgroup. Numbers in parentheses indicate the total FSFs in each viral subgroup. White circles indicate group medians. A density trace is plotted symmetrically around the boxplots.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643759&req=5

Figure 6: Ancient history of RNA viral proteomes.(A) The length of Ariadne’s threads (colored lines) identifies FSFs that were shared by more than three viral subgroups. Filled circles indicate FSFs shared between two or three viral subgroups. Numbers next to each circle give the mean nd of FSFs shared by each combination. Numbers in parentheses give the range between the most ancient and the most recent FSFs that were shared by each combination. (B) Distribution of the most ancient (nd < 0.3) ABEV FSFs in evolutionary timeline (nd) for each viral subgroup. Numbers in parentheses indicate the total FSFs in each viral subgroup. White circles indicate group medians. A density trace is plotted symmetrically around the boxplots.
Mentions: (ii) Ariadne’s threads traced in evolutionary time. We traced FSF domain ages onto the threads of FSFs shared between viral subgroups (Fig. 6A). The oldest domains were spread in a transect that unified minus-ssRNA, plus-ssRNA, and dsRNA proteomes. This pattern was clearly evident in violin plots that describe FSF age in the threads along the early timeline of domain evolution (nd < 0.3) (Fig. 6B). Once again, the proteomes of minus-ssRNA viruses were particularly enriched in ancient domains, suggesting that perhaps ssRNA was involved in virocell origins (read below).

Bottom Line: Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data.Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the "viral supergroup" and the existence of widespread episodes of horizontal transfer of genetic information.Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA.

ABSTRACT
The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the "viral supergroup" and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts.

No MeSH data available.


Related in: MedlinePlus