title: Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses.
abstract: Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses.
authors.affiliation: Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.|Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, United States of America.
authors.forename: Lauro
authors.initials: L
authors.lastname: Velazquez-Salinas
authors.affiliation: Autonomous University of Mexico City, Genomics Sciences Program, Mexico City, Mexico.
authors.forename: Selene
authors.initials: S
authors.lastname: Zarate
authors.affiliation: Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.|Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Eschbaumer
authors.affiliation: Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa) Campinas, Brazil.
authors.forename: Francisco
authors.initials: F
authors.lastname: Pereira Lobo
authors.affiliation: Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.
authors.forename: Douglas P
authors.initials: DP
authors.lastname: Gladue
authors.affiliation: Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Arzt
authors.affiliation: Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, Toledo, Ohio, United States of America.
authors.forename: Isabel S
authors.initials: IS
authors.lastname: Novella
authors.affiliation: Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.
authors.forename: Luis L
authors.initials: LL
authors.lastname: Rodriguez
mesh_terms: D000596:Amino Acids; D001102:Arbovirus Infections / Q000821:virology; D001103:Arboviruses / Q000235:genetics*; D001482:Base Composition; D015415:Biomarkers; D016000:Cluster Analysis; D003062:Codon; D019143:Evolution, Molecular; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D054884:Host-Pathogen Interactions; D012641:Selection, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics; D056189:Viral Tropism
chemical_list: D000596:Amino Acids; D015415:Biomarkers; D003062:Codon; D014764:Viral Proteins