Tags

Type your tag names separated by a space and hit enter

Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution.
Virol J. 2009 Dec 17; 6:223.VJ

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.

Authors+Show Affiliations

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. yutin@ncbi.nlm.nih.govNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, N.I.H., Intramural

Language

eng

PubMed ID

20017929

Citation

Yutin, Natalya, et al. "Eukaryotic Large Nucleo-cytoplasmic DNA Viruses: Clusters of Orthologous Genes and Reconstruction of Viral Genome Evolution." Virology Journal, vol. 6, 2009, p. 223.
Yutin N, Wolf YI, Raoult D, et al. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J. 2009;6:223.
Yutin, N., Wolf, Y. I., Raoult, D., & Koonin, E. V. (2009). Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virology Journal, 6, 223. https://doi.org/10.1186/1743-422X-6-223
Yutin N, et al. Eukaryotic Large Nucleo-cytoplasmic DNA Viruses: Clusters of Orthologous Genes and Reconstruction of Viral Genome Evolution. Virol J. 2009 Dec 17;6:223. PubMed PMID: 20017929.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. AU - Yutin,Natalya, AU - Wolf,Yuri I, AU - Raoult,Didier, AU - Koonin,Eugene V, Y1 - 2009/12/17/ PY - 2009/10/27/received PY - 2009/12/17/accepted PY - 2009/12/19/entrez PY - 2009/12/19/pubmed PY - 2010/3/26/medline SP - 223 EP - 223 JF - Virology journal JO - Virol J VL - 6 N2 - 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. SN - 1743-422X UR - https://www.unboundmedicine.com/medline/citation/20017929/Eukaryotic_large_nucleo_cytoplasmic_DNA_viruses:_clusters_of_orthologous_genes_and_reconstruction_of_viral_genome_evolution_ L2 - https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-6-223 DB - PRIME DP - Unbound Medicine ER -