G + C content differs in conserved and variable amino acid residues of flaviviruses and other evolutionary groups

Banerjee, 2005, Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms, Biosystems, 81, 11, 10.1016/j.biosystems.2005.01.002 Belalov, 2013, Causes and implications of codon usage bias in RNA viruses, PLoS One, 8, 10.1371/journal.pone.0056642 Bellgard, 1999, Inferring the direction of evolutionary changes of genomic base composition, Trends Genet., 15, 254, 10.1016/S0168-9525(99)01760-6 Bellgard, 1999, Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content, Gene, 238, 33, 10.1016/S0378-1119(99)00318-2 Calisher, 2003, Taxonomy of the virus family Flaviviridae, Adv. Virus Res., 59, 1, 10.1016/S0065-3527(03)59001-7 Calisher, 1989, Antigenic relationships between flaviviruses as determined by cross-neutralization tests with polyclonal antisera, J Gen Virol, 70, 37, 10.1099/0022-1317-70-1-37 Cook, 2006, A multigene analysis of the phylogenetic relationships among the flaviviruses (family: Flaviviridae) and the evolution of vector transmission, Arch. Virol., 151, 309, 10.1007/s00705-005-0626-6 de Lamballerie, 2002, Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus, J. Gen. Virol., 83, 2443, 10.1099/0022-1317-83-10-2443 Di Giulio, 1989, The extension reached by the minimization of the polarity distances during the evolution of the genetic code, J. Mol. Evol., 29, 288, 10.1007/BF02103616 D'Onofrio, 1999, The correlation of protein hydropathy with the base composition of coding sequences, Gene, 238, 3, 10.1016/S0378-1119(99)00257-7 England, 2013, Statistical physics of self-replication, J. Chem. Phys., 139, 121923, 10.1063/1.4818538 Freeland, 1998, The genetic code is one in a million, J. Mol. Evol., 47, 238, 10.1007/PL00006381 Gaunt, 2001, Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography, J Gen Virol, 82, 1867, 10.1099/0022-1317-82-8-1867 Gu, 1998, Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria, Genetica, 102-103, 383, 10.1023/A:1017028102013 Hammon, 1960, Viruses associated with epidemic hemorrhagic fevers of the Philippines and Thailand, Science, 131, 1102, 10.1126/science.131.3407.1102 Jabbari, 2003, The correlation between GC3 and hydropathy in human genes, Gene, 317, 137, 10.1016/S0378-1119(03)00663-2 Jenkins, 2003, The extent of codon usage bias in human RNA viruses and its evolutionary origin, Virus Res., 92, 1, 10.1016/S0168-1702(02)00309-X Jenkins, 2001, Evolution of base composition and codon usage bias in the genus Flavivirus, J. Mol. Evol., 52, 383, 10.1007/s002390010168 Kitchen, 2011, Family level phylogenies reveal modes of macroevolution in RNA viruses, Proc. Natl. Acad. Sci. U. S. A., 108, 238, 10.1073/pnas.1011090108 Kuno, 1998, Phylogeny of the genus Flavivirus, J. Virol., 72, 73, 10.1128/JVI.72.1.73-83.1998 Li, 2015, GC-content of synonymous codons profoundly influences amino acid usage, G3 (Bethesda), 5, 2027, 10.1534/g3.115.019877 Lobo, 2009, Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts, PLoS One, 4, 10.1371/journal.pone.0006282 Lobry, 1997, Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species, Gene, 205, 309, 10.1016/S0378-1119(97)00403-4 Moureau, 2015, New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences, PLoS One, 10, 10.1371/journal.pone.0117849 Perelman, 2011, A molecular phylogeny of living primates, PLoS Genet., 7, 10.1371/journal.pgen.1001342 Sabin, 1952, Research on dengue during World War II, Am.J.Trop. Med. Hyg., 1, 30, 10.4269/ajtmh.1952.1.30 Schubert, 2010, Evolution of the sequence composition of Flaviviruses, Infect. Genet. Evol., 10, 129, 10.1016/j.meegid.2009.11.004 Singer, 2000, Nucleotide bias causes a genomewide bias in the amino acid composition of proteins, Mol. Biol. Evol., 17, 1581, 10.1093/oxfordjournals.molbev.a026257 Smith, 1938, Yellow fever vaccination with cultured virus (17D) without immune serum, American Journal of Tropical Medicine, 18, 437, 10.4269/ajtmh.1938.s1-18.437 Sueoka, 1962, On the genetic basis of variation and heterogeneity of DNA base composition, Proc. Natl. Acad. Sci. U. S. A., 48, 582, 10.1073/pnas.48.4.582 Sueoka, 1988, Directional mutation pressure and neutral molecular evolution, Proc. Natl. Acad. Sci. U. S. A., 85, 2653, 10.1073/pnas.85.8.2653 Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197 Taylor, 1989, The code within the codons, Biosystems, 22, 177, 10.1016/0303-2647(89)90059-2 Team, 2013 Virus Taxonomy, 2014 Wong, 1980, Role of minimization of chemical distances between amino acids in the evolution of the genetic code, Proc. Natl. Acad. Sci. U. S. A., 77, 1083, 10.1073/pnas.77.2.1083