@article{fdi:010049217,
  title = {{E}ukaryotic large nucleo-cytoplasmic {DNA} viruses : clusters of orthologous genes and reconstruction of viral genome evolution},
  author = {{Y}utin, {N}. and {W}olf, {Y}. {I}. and {R}aoult, {D}idier and {K}oonin, {E}. {V}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}he {N}ucleo-{C}ytoplasmic {L}arge {DNA} {V}iruses ({NCLDV}) comprise an apparently monophyletic class of viruses that infect a broad variety of eukaryotic hosts. {R}ecent 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. {R}esults: {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. {U}sing previously developed computational methods for orthology identification, 1445 {N}ucleo-{C}ytoplasmic {V}irus {O}rthologous {G}roups ({NCVOG}s) were identified of which 177 are represented in more than one {NCLDV} family. {T}he {NCVOG}s 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. {T}his 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. {C}onclusions: {T}he {NCVOG}s are a flexible and expandable platform for genome analysis and functional annotation of newly characterized {NCLDV}. {E}volutionary reconstructions employing {NCVOG}s point to complex ancestral viruses.},
  keywords = {},
  booktitle = {},
  journal = {{V}irology {J}ournal},
  volume = {6},
  numero = {},
  pages = {223},
  ISSN = {1743-422{X}},
  year = {2009},
  DOI = {10.1186/1743-422x-6-223},
  URL = {https://www.documentation.ird.fr/hor/fdi:010049217},
}