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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.

SUBMITTER: Lara-Ramirez EE 

PROVIDER: S-EPMC4124757 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence.

Lara-Ramírez Edgar E EE   Salazar Ma Isabel MI   López-López María de Jesús Mde J   Salas-Benito Juan Santiago JS   Sánchez-Varela Alejandro A   Guo Xianwu X  

BioMed research international 20140717


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 mutationa  ...[more]

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