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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

Evolutionary history of proteomes inferred from numerical analysis.(A) Plot of the first three axes of evoPCO portrays evolutionary distances between cellular and viral proteomes. The percentage of variability explained by each coordinate is given in parentheses on each axis. The proteome of the last common ancestor of modern cells (57) was added as an additional sample to infer the direction of evolutionary splits. aIgnicoccus hospitalis, bLactobacillus delbrueckii, cCaenorhabditis elegans. (B) A distance-based NJ tree reconstructed from the occurrence of 442 ABEV FSFs in randomly sampled 368 proteomes. Each taxon was given a unique tree ID (tables S1 and S2). Taxa were colored for quick visualization.
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Figure 8: Evolutionary history of proteomes inferred from numerical analysis.(A) Plot of the first three axes of evoPCO portrays evolutionary distances between cellular and viral proteomes. The percentage of variability explained by each coordinate is given in parentheses on each axis. The proteome of the last common ancestor of modern cells (57) was added as an additional sample to infer the direction of evolutionary splits. aIgnicoccus hospitalis, bLactobacillus delbrueckii, cCaenorhabditis elegans. (B) A distance-based NJ tree reconstructed from the occurrence of 442 ABEV FSFs in randomly sampled 368 proteomes. Each taxon was given a unique tree ID (tables S1 and S2). Taxa were colored for quick visualization.

Mentions: (v) ToP derived directly from the age of protein domains. We also developed a multidimensional scaling approach to study the evolution of cells and viruses: the evolutionary principal coordinate (evoPCO) analysis (Fig. 8A). The evoPCO method combines the power of cladistic and phenetic approaches by calculating principal coordinates directly from temporal evolutionary distances between the proteomes of species (see Materials and Methods). The distance between proteomes reflects phylogenetic dissimilarity in the age of FSF domain repertoires (that is, nd values) and can be displayed in 3D temporal space, assuming that the age of an FSF is the age of the first instance of that FSF appearing in evolution. Because proteomes are biological systems that are made up of component parts (that is, FSFs in this case) but describe cellular organisms and viruses, each component (regardless of its abundance) contributes an age to the overall age of the cellular or viral system. This factor, when taken into account, results in a powerful projection of a multidimensional space of proteomes onto a 3D temporal space that allows visualization of evolutionary relationships.


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

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

Evolutionary history of proteomes inferred from numerical analysis.(A) Plot of the first three axes of evoPCO portrays evolutionary distances between cellular and viral proteomes. The percentage of variability explained by each coordinate is given in parentheses on each axis. The proteome of the last common ancestor of modern cells (57) was added as an additional sample to infer the direction of evolutionary splits. aIgnicoccus hospitalis, bLactobacillus delbrueckii, cCaenorhabditis elegans. (B) A distance-based NJ tree reconstructed from the occurrence of 442 ABEV FSFs in randomly sampled 368 proteomes. Each taxon was given a unique tree ID (tables S1 and S2). Taxa were colored for quick visualization.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Evolutionary history of proteomes inferred from numerical analysis.(A) Plot of the first three axes of evoPCO portrays evolutionary distances between cellular and viral proteomes. The percentage of variability explained by each coordinate is given in parentheses on each axis. The proteome of the last common ancestor of modern cells (57) was added as an additional sample to infer the direction of evolutionary splits. aIgnicoccus hospitalis, bLactobacillus delbrueckii, cCaenorhabditis elegans. (B) A distance-based NJ tree reconstructed from the occurrence of 442 ABEV FSFs in randomly sampled 368 proteomes. Each taxon was given a unique tree ID (tables S1 and S2). Taxa were colored for quick visualization.
Mentions: (v) ToP derived directly from the age of protein domains. We also developed a multidimensional scaling approach to study the evolution of cells and viruses: the evolutionary principal coordinate (evoPCO) analysis (Fig. 8A). The evoPCO method combines the power of cladistic and phenetic approaches by calculating principal coordinates directly from temporal evolutionary distances between the proteomes of species (see Materials and Methods). The distance between proteomes reflects phylogenetic dissimilarity in the age of FSF domain repertoires (that is, nd values) and can be displayed in 3D temporal space, assuming that the age of an FSF is the age of the first instance of that FSF appearing in evolution. Because proteomes are biological systems that are made up of component parts (that is, FSFs in this case) but describe cellular organisms and viruses, each component (regardless of its abundance) contributes an age to the overall age of the cellular or viral system. This factor, when taken into account, results in a powerful projection of a multidimensional space of proteomes onto a 3D temporal space that allows visualization of evolutionary relationships.

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