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Published on: July 27, 2018
Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses
Adam Monier1, Jean-Michel Claverie, Hiroyuki Ogata
1Structural and Genomic Information Laboratory, CNRS - UPR 2589, Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, 163 avenue de Luminy, FR-13288, Marseille cedex 09, France. Adam.Monier@igs.cnrs-mrs.fr
BMC Genomics
|December 12, 2007
Summary
Large DNA viruses do not frequently acquire genes from modern hosts, challenging the "gene pickpocket" theory. Their large genome sizes are not solely due to gene acquisition, and anomalous gene compositions may be misidentified as horizontal transfers.
Area of Science:
- Virology
- Genomics
- Bioinformatics
Background:
- Large DNA viruses exhibit significant genome size variation unrelated to host or virulence.
- The traditional view suggests large viral genomes arise from extensive gene acquisition from hosts.
- Understanding the drivers of viral genome size variation is crucial.
Purpose of the Study:
- To investigate the hypothesis of frequent gene acquisition in large DNA viruses.
- To analyze the compositional properties of viral genomes and identify anomalous genes.
- To determine the origins and implications of compositional heterogeneity in viral genomes.
Main Methods:
- Studied 67 large DNA viruses (>150 kb genomes).
- Analyzed inter- and intra-genome nucleotide composition and word usage.
- Employed Bayesian inference to identify compositionally anomalous (cA) genes.
- Interpreted compositional heterogeneity considering strand asymmetry, gene function, and horizontal transfer.
Main Results:
- Viral genome composition is species-specific and distinct from hosts.
- The proportion of cA genes varies widely and doesn't correlate with genome size.
- Most cA genes lack known homologs; some with homologs show functional enrichment.
- Phylogenetic analysis confirmed exogenous origin for a small fraction of cA genes.
Conclusions:
- Evidence argues against frequent recent gene transfers from hosts to large DNA viruses.
- Large viral genome size is not solely explained by increased foreign gene acquisition.
- Anomalous gene composition can be linked to biological functions, not just horizontal transfer, potentially leading to overestimation of gene transfers.
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