Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence
Joint Authors
Lara-Ramírez, Edgar E.
Salazar, Ma. Isabel
Guo, Xianwu
Salas-Benito, Juan Santiago
López-López, María de Jesús
Sánchez-Varela, Alejandro
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-07-17
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Lara-Ramírez, Edgar E.& Salazar, Ma. Isabel& López-López, María de Jesús& Salas-Benito, Juan Santiago& Sánchez-Varela, Alejandro& Guo, Xianwu. 2014. Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence. BioMed Research International،Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-503308
Modern Language Association (MLA)
Lara-Ramírez, Edgar E.…[et al.]. Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence. BioMed Research International No. 2014 (2014), pp.1-9.
https://search.emarefa.net/detail/BIM-503308
American Medical Association (AMA)
Lara-Ramírez, Edgar E.& Salazar, Ma. Isabel& López-López, María de Jesús& Salas-Benito, Juan Santiago& Sánchez-Varela, Alejandro& Guo, Xianwu. Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-503308
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-503308