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Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution.

Yutin N, Wolf YI, Raoult D, Koonin EV - Virol. J. (2009)

Bottom Line: A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes.The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes.The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. yutin@ncbi.nlm.nih.gov

ABSTRACT

Background: The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) comprise an apparently monophyletic class of viruses that infect a broad variety of eukaryotic hosts. Recent progress in isolation of new viruses and genome sequencing resulted in a substantial expansion of the NCLDV diversity, resulting in additional opportunities for comparative genomic analysis, and a demand for a comprehensive classification of viral genes.

Results: A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes. Using previously developed computational methods for orthology identification, 1445 Nucleo-Cytoplasmic Virus Orthologous Groups (NCVOGs) were identified of which 177 are represented in more than one NCLDV family. The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes. A maximum-likelihood reconstruction of the NCLDV evolution yielded a set of 47 conserved genes that were probably present in the genome of the common ancestor of this class of eukaryotic viruses. This reconstructed ancestral gene set is robust to the parameters of the reconstruction procedure and so is likely to accurately reflect the gene core of the ancestral NCLDV, indicating that this virus encoded a complex machinery of replication, expression and morphogenesis that made it relatively independent from host cell functions.

Conclusions: The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV. Evolutionary reconstructions employing NCVOGs point to complex ancestral viruses.

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Functional classification of the 177 NCVOGs that include two or more NCLDV families.
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Figure 6: Functional classification of the 177 NCVOGs that include two or more NCLDV families.

Mentions: The 177 multifamily NCVOGs were annotated with respect to the known or predicted functions and assigned to several broad functional classes (Figure 6 and Additional File 1). Notably, the widespread NCVOGs consist of genes that encode proteins involved in key functions of viral replication and morphogenesis as is typical of viral hallmark genes (Additional File 1). It is also of note that among the 177 widespread NCVOGs there are virtually none without an assigned function (at least in general terms; Additional File 1). Thus, transfer of functional information from experimentally characterized viral genes to uncharacterized orthologs in other viruses yields a fairly complete compendium of the core NCLDV functions.


Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution.

Yutin N, Wolf YI, Raoult D, Koonin EV - Virol. J. (2009)

Functional classification of the 177 NCVOGs that include two or more NCLDV families.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2806869&req=5

Figure 6: Functional classification of the 177 NCVOGs that include two or more NCLDV families.
Mentions: The 177 multifamily NCVOGs were annotated with respect to the known or predicted functions and assigned to several broad functional classes (Figure 6 and Additional File 1). Notably, the widespread NCVOGs consist of genes that encode proteins involved in key functions of viral replication and morphogenesis as is typical of viral hallmark genes (Additional File 1). It is also of note that among the 177 widespread NCVOGs there are virtually none without an assigned function (at least in general terms; Additional File 1). Thus, transfer of functional information from experimentally characterized viral genes to uncharacterized orthologs in other viruses yields a fairly complete compendium of the core NCLDV functions.

Bottom Line: A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes.The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes.The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. yutin@ncbi.nlm.nih.gov

ABSTRACT

Background: The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) comprise an apparently monophyletic class of viruses that infect a broad variety of eukaryotic hosts. Recent progress in isolation of new viruses and genome sequencing resulted in a substantial expansion of the NCLDV diversity, resulting in additional opportunities for comparative genomic analysis, and a demand for a comprehensive classification of viral genes.

Results: A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes. Using previously developed computational methods for orthology identification, 1445 Nucleo-Cytoplasmic Virus Orthologous Groups (NCVOGs) were identified of which 177 are represented in more than one NCLDV family. The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes. A maximum-likelihood reconstruction of the NCLDV evolution yielded a set of 47 conserved genes that were probably present in the genome of the common ancestor of this class of eukaryotic viruses. This reconstructed ancestral gene set is robust to the parameters of the reconstruction procedure and so is likely to accurately reflect the gene core of the ancestral NCLDV, indicating that this virus encoded a complex machinery of replication, expression and morphogenesis that made it relatively independent from host cell functions.

Conclusions: The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV. Evolutionary reconstructions employing NCVOGs point to complex ancestral viruses.

Show MeSH
Related in: MedlinePlus