title: Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence.
abstract: The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1-4 (DENV1-4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1-4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution.
authors.affiliation: Laboratory of Molecular Biomedicine, Center of Biotechnology on Genomics, National Polytechnic Institute, Colonia Narciso Mendoza, 88710 Reynosa, TAMPS, Mexico.
authors.forename: Edgar E
authors.initials: EE
authors.lastname: Lara-Ramírez
authors.affiliation: Laboratory for Cellular Immunology and Immunopathogenesis, Department of Immunology, National School for Biological Sciences (ENCB), National Polytechnic Institute, 11340 New Mexico, DF, Mexico.
authors.forename: Ma Isabel
authors.initials: MI
authors.lastname: Salazar
authors.affiliation: Laboratory of Molecular Biomedicine, Center of Biotechnology on Genomics, National Polytechnic Institute, Colonia Narciso Mendoza, 88710 Reynosa, TAMPS, Mexico.
authors.forename: María de Jesús
authors.initials: Mde J
authors.lastname: López-López
authors.affiliation: Laboratory for Biomedicine, Department of Virology, National School of Medicine and Homeopathy, National Polytechnic Institute, 11340 New Mexico, DF, Mexico.
authors.forename: Juan Santiago
authors.initials: JS
authors.lastname: Salas-Benito
authors.affiliation: Laboratory of Molecular Biomedicine, Center of Biotechnology on Genomics, National Polytechnic Institute, Colonia Narciso Mendoza, 88710 Reynosa, TAMPS, Mexico.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sánchez-Varela
authors.affiliation: Laboratory of Molecular Biomedicine, Center of Biotechnology on Genomics, National Polytechnic Institute, Colonia Narciso Mendoza, 88710 Reynosa, TAMPS, Mexico.
authors.forename: Xianwu
authors.identifier: 0000-0003-2013-5853
authors.initials: X
authors.lastname: Guo
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D003715:Dengue / Q000235:genetics / Q000821:virology; D003716:Dengue Virus / Q000235:genetics*; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D009154:Mutation; D010802:Phylogeny
chemical_list: D003062:Codon