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Unique genes in giant viruses: regular substitution pattern and anomalously short size.
Genome Res. 2007 Sep; 17(9):1353-61.GR

Abstract

Large DNA viruses, including giant mimivirus with a 1.2-Mb genome, exhibit numerous orphan genes possessing no database homologs or genes with homologs solely in close members of the same viral family. Due to their solitary nature, the functions and evolutionary origins of those genes remain obscure. We examined sequence features and evolutionary rates of viral family-specific genes in three nucleo-cytoplasmic large DNA virus (NCLDV) lineages. First, we showed that the proportion of family-specific genes does not correlate with sequence divergence rate. Second, position-dependent nucleotide statistics were similar between family-specific genes and the remaining genes in the genome. Third, we showed that the synonymous-to-nonsynonymous substitution ratios in those viruses are at levels comparable to those estimated for vertebrate proteomes. Thus, the vast majority of family-specific genes do not exhibit an accelerated evolutionary rate, and are thus likely to specify functional polypeptides. On the other hand, these family-specific proteins exhibit several distinct properties: (1) they are shorter, (2) they include a larger fraction of predicted transmembrane proteins, and (3) they are enriched in low-complexity sequences. These results suggest that family-specific genes do not correspond to recent horizontal gene transfer. We propose that their characteristic features are the consequences of the specific evolutionary forces shaping the viral gene repertoires in the context of their parasitic lifestyles.

Authors+Show Affiliations

Structural and Genomic Information Laboratory CNRS-UPR 2589, IBSM Parc Scientifique de Luminy, Case 934 13288 Marseille Cedex 9, France. Hiroyuki.Ogata@igs.cnrs-mrs.frNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17652424

Citation

Ogata, Hiroyuki, and Jean-Michel Claverie. "Unique Genes in Giant Viruses: Regular Substitution Pattern and Anomalously Short Size." Genome Research, vol. 17, no. 9, 2007, pp. 1353-61.
Ogata H, Claverie JM. Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Res. 2007;17(9):1353-61.
Ogata, H., & Claverie, J. M. (2007). Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Research, 17(9), 1353-61.
Ogata H, Claverie JM. Unique Genes in Giant Viruses: Regular Substitution Pattern and Anomalously Short Size. Genome Res. 2007;17(9):1353-61. PubMed PMID: 17652424.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Unique genes in giant viruses: regular substitution pattern and anomalously short size. AU - Ogata,Hiroyuki, AU - Claverie,Jean-Michel, Y1 - 2007/07/25/ PY - 2007/7/27/pubmed PY - 2007/11/2/medline PY - 2007/7/27/entrez SP - 1353 EP - 61 JF - Genome research JO - Genome Res VL - 17 IS - 9 N2 - Large DNA viruses, including giant mimivirus with a 1.2-Mb genome, exhibit numerous orphan genes possessing no database homologs or genes with homologs solely in close members of the same viral family. Due to their solitary nature, the functions and evolutionary origins of those genes remain obscure. We examined sequence features and evolutionary rates of viral family-specific genes in three nucleo-cytoplasmic large DNA virus (NCLDV) lineages. First, we showed that the proportion of family-specific genes does not correlate with sequence divergence rate. Second, position-dependent nucleotide statistics were similar between family-specific genes and the remaining genes in the genome. Third, we showed that the synonymous-to-nonsynonymous substitution ratios in those viruses are at levels comparable to those estimated for vertebrate proteomes. Thus, the vast majority of family-specific genes do not exhibit an accelerated evolutionary rate, and are thus likely to specify functional polypeptides. On the other hand, these family-specific proteins exhibit several distinct properties: (1) they are shorter, (2) they include a larger fraction of predicted transmembrane proteins, and (3) they are enriched in low-complexity sequences. These results suggest that family-specific genes do not correspond to recent horizontal gene transfer. We propose that their characteristic features are the consequences of the specific evolutionary forces shaping the viral gene repertoires in the context of their parasitic lifestyles. SN - 1088-9051 UR - https://www.unboundmedicine.com/medline/citation/17652424/Unique_genes_in_giant_viruses:_regular_substitution_pattern_and_anomalously_short_size_ L2 - http://genome.cshlp.org:4040/lookup/pmidlookup?view=long&pmid=17652424 DB - PRIME DP - Unbound Medicine ER -