Analysis Of Codon Usage Bias And Influencing Factors In The Genomes Of Rice Tungro Bacilliform And Yellow Mottle Virus

Rice tungro bacilliform virus(RTBV)and Rice yellow mottle virus(RYMV)both are the major viral constraint to rice production.Rice tungro bacilliform virus(RTBV)belongs to the family Caulimoviridae harbors circular double-stranded DNA(dsDNA).While the Rice yellow mottle virus(RYMV)is a member of the family Solemoviridae harbors single-stranded positivesense RNA(ssRNA)genome.Both viruses use insects as a vector which cause infection in rice with a wide range and create economic problem.The virus causes Rice tungro disease(RTD),responsible for severe rice yield losses in South and Southeast Asia.There is an increasing rice health concern about the virus infection.The purpose of this study was to determine the influences of viral relationships with their hosts on viral fitness,survival,and evasion from host defense systems.In this study,we performed a comprehensive study to explore its evolution,adaptation in host,and determined primary forces that affect the codon usage bias in the RTBV and RYMV genome.We analyzed different bioinformatics techniques to calculate the nucleotide compositions,the relative synonymous codon usage(RSCU),the effective number of codons(ENC),codon adaptation index(CAI),and other indices.There are several results obtained from various analysis.Although using the same methods for both studies,we obtained slightly different results which shows that each genome has its own codon bias signature.The results indicated slightly or low codon usage bias in RTBV/RYMV isolates.Various approaches suggested that both mutation and natural selection pressures have equally contributed to this low codon usage bias viruses.Additionally,multiple factors such as host,base composition,aromaticity,hydrophobicity,and geographical distribution may also affect codon usage patterns in RTBV/RYMV virus genomes.The RSCU analysis revealed that RTBV genomes preferred A and U ended codons,whereas the RYMV preferred the G and C ended codons to code the amino acids.Codon usage patterns of the viruses were also found to be influenced by its host.This indicates that both viruses have evolved codon usage patterns that are specific to its hosts.The findings from this study are likely to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.Furthermore,this study also helps in a better and deep understanding of the evolutionary processes of viruses that will serve its future basic research and drugs design.