Synonymous Codon Pattern of Cauliflower Mosaic Virus in phylogeny and evolution

Abstract

Cauliflower Mosaic Virus (CaMV) is a plant Pararetrovirus with a double-stranded DNA genome distributed worldwide. This study analyzed migration, evolution, and synonymous codon pattern of CaMV and the factors that shape it. We extracted genomic sequences of 121 isolates of CaMV, which were reported from various regions-hosts, from the NCBI database. The evolution of viruses has been widely studied by analyzing their nucleotides and coding regions/codons using different methods. Analysis of the CaMV phylogenetic tree shows that it divides most of the sequences into two main groups: Group I includes Irananin, Japanese, and American-European subgroups, and Group II includes Grecian, Turkish, and Iranian subgroups. Analysis of effective codon count, and relative codon deoptimization index, showed that natural selection is a major driving force in CaMV. Furthermore, Relative synonymous codon usage (RSCU) and neutrality analyses show that CaMV prefers A-ending codons and that one codon, namely GGA, was overrepresented. Analysis of dinucleotide composition demonstrates that nucleotide A was the most abundant in the CaMV coding sequences, and that the most frequent nucleotide at the third position of the codon was A3S. In CaMV, host adaptation was highest for Brassica oleracea and lowest for Raphanus sativus. Therefore the CaMV codon pattern is mostly shaped by the need to escape antiviral responses associated with host dinucleotides and translational efficiency. These values indicate that the study provides useful information on the codon usage analysis of CaMV and can be used to understand host adaptation to the virus environment and its evolution. This is the first study on codon usage bias of CaMV in the world.