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Title: Dengue virus type 4 evolution and genomics: A bioinformatic approach
Authors: Pal, Shilpee
Banerjee, Amrita
Das, Partha Sarathi
Pati, Bikas R
Mandal, Keshab C
Chakraborty, Biplab
Sen, Arnab
Mohapatra, Pradeep K Das
Keywords: Compositional constraint;Correspondence analysis;Dengue virus type 4;Highly expressed gene;Relative synonymous codon usage;Mutational bias
Issue Date: Jul-2014
Publisher: NISCAIR-CSIR, India
Abstract: Dengue is becoming the most devastating endemic disease in the last few years all over the world. Four serotypes DENV1, DENV2, DENV3 and DENV4 show strong adaptation against host defence. DENV4 is phylogenetically most divergent serotype and highlights the importance of the study about evolution and genomics of DENV4 genome. Overall, study of codon usage pattern at gene level and the effect of mutational bias, natural selection, translational selection and gene length were estimated. A multivariate statistical analysis showed the conservation of codon usage pattern among phylogenetically closely related DENV4 genomes. For compositional constraint, most of the preferred codons in DENV4 genes contain ‘A’ and/or ‘T’ at 3rd position. Moreover, mutational bias and gene length were also functioning for the variation in codon usage. Pyrimidines ending preferred codons were slightly numerous in highly expressed genes, but codon usage bias was higher in non-structural genes than structural one, which was the evidence for the absence of the effect of translational selection on codon usage variation of DENV4 genome. The study is helpful to understand the evolution of DENV4 genome and gradual change in their pathogenicity.
Page(s): 330-336
ISSN: 0975-0967 (Online); 0972-5849 (Print)
Appears in Collections:IJBT Vol.13(3) [July 2014]

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