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BioMed Research International
Volume 2014, Article ID 851425, 9 pages
Research Article

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

1Laboratory of Molecular Biomedicine, Center of Biotechnology on Genomics, National Polytechnic Institute, Colonia Narciso Mendoza, 88710 Reynosa, TAMPS, Mexico
2Laboratory for Cellular Immunology and Immunopathogenesis, Department of Immunology, National School for Biological Sciences (ENCB), National Polytechnic Institute, 11340 New Mexico, DF, Mexico
3Laboratory for Biomedicine, Department of Virology, National School of Medicine and Homeopathy, National Polytechnic Institute, 11340 New Mexico, DF, Mexico

Received 25 February 2014; Revised 5 June 2014; Accepted 11 June 2014; Published 17 July 2014

Academic Editor: Sankar Subramanian

Copyright © 2014 Edgar E. Lara-Ramírez et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.