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Decoding of Codon Usage Patterns of Two Betaflexiviruses Cherry Virus A and Prunus Virus T
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چکیده: (7 مشاهده) |
Background and Aims: Among the more than fifty viruses that infect stone fruit trees and belong to the Betaflexiviridae family, cherry virus A (Capillovirus) and prunus virus T (Tepovirus) are common members. In this study, we provide codon usage analyses and composition of CVA and PrVT based on their full genome nucleotide sequences. Codon usage patterns studies provide great information about host-pathogen co-evolution, phylogenetic relations among specific species, and molecular evolution of genes.
Material and methods: Genome sequences of CVA and PrVT isolates available at GenBank including two Iranian isolates from sweet cherry were used for nucleotide composition analysis using MEGAX soft-ware. The nucleotide mixtures at the 3rd codon position (A3s, C3s, T3s, G3s%, and GC3s), were determined using CodonW 1.4.2 package (http://codonw.sourceforge.net). The RSCU values for the ORFs coding sequences were determined to explore aspects of synonymous codon usage without the complex influence of amino acid composition and coding sequence size of samples. The ENC value was determined using Codon W v1.4.2. ENC analysis was used to quantify the absolute codon usage bias by evaluating the degree of codon usage bias exhibited by the coding sequences, regardless of gene length and the number of amino acids.
Results: Our analysis indicates synonymous codon usage in CVA and PrVT possibly mirroring a dynamic process of mutations from the viruses along with selection pressure to adjust their codon usage to various hosts, and conditions. Furthermore, relative synonymous codon usage-RSCU, nucleotide composition, and an effective number of codon-ENC-plots analysis results suggest that the selection pressure was greater than mutation pressure.
Conclusions: This bioinformatics analysis expands our knowledge of the differences and common features in codon usage patterns of betaflexiviruses with their various hosts. |
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متن کامل [PDF 813 kb]
(4 دریافت)
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نوع مطالعه: پژوهشي |
موضوع مقاله:
عمومى
دریافت: 1403/12/11 | پذیرش: 1403/9/20 | انتشار: 1403/9/20
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