Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses Export

@article{citeulike:3058317, abstract = {Abstract\ \ Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting DNA viruses. This revealed that patterns of codon usage bias are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational pressure, rather than natural selection for specific coding triplets, is the main determinant of codon usage. Further, we observed a striking difference in CpG content between DNA viruses with large and small genomes. While the majority of large genome viruses show the expected frequency of CpG, most small genome viruses had CpG contents far below expected values. The exceptions to this generalization, the large gammaherpesviruses and iridoviruses and the small dependoviruses, have sufficiently different life-cycle characteristics that they may help reveal some of the factors shaping the evolution of CpG usage in viruses.}, author = {Shackelton, Laura and Parrish, Colin and Holmes, Edward}, citeulike-article-id = {3058317}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00239-005-0221-1}, day = {1}, doi = {10.1007/s00239-005-0221-1}, journal = {Journal of Molecular Evolution}, keywords = {cpg, cpg\_suppression, dna, virus}, month = {May}, number = {5}, pages = {551--563}, posted-at = {2008-07-30 03:49:01}, priority = {2}, title = {Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses}, url = {http://dx.doi.org/10.1007/s00239-005-0221-1}, volume = {62}, year = {2006} }

TY - JOUR ID - citeulike:3058317 L3 - citeulike-article-id:3058317 N2 - Abstract  Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting DNA viruses. This revealed that patterns of codon usage bias are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational pressure, rather than natural selection for specific coding triplets, is the main determinant of codon usage. Further, we observed a striking difference in CpG content between DNA viruses with large and small genomes. While the majority of large genome viruses show the expected frequency of CpG, most small genome viruses had CpG contents far below expected values. The exceptions to this generalization, the large gammaherpesviruses and iridoviruses and the small dependoviruses, have sufficiently different life-cycle characteristics that they may help reveal some of the factors shaping the evolution of CpG usage in viruses. IS - 5 JF - Journal of Molecular Evolution EP - 563 TI - Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses VL - 62 SP - 551 KW - cpg KW - cpg_suppression KW - dna KW - virus AU - Shackelton, Laura AU - Parrish, Colin AU - Holmes, Edward PY - 2006/05/01/ UR - http://dx.doi.org/10.1007/s00239-005-0221-1 ER -