The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species

Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases

“…(ii) Genetic drift is a key factor on the evolution of viruses, while the effect of drift on the CUB of plant RNA viruses is unclear. (iii) For single strand plant RNA viruses, the genes or coding protein regions of viruses appeared more stronger effect than host tRNA selection on their nucleotide, and dinucleotide composition [40] , [59] , [60] , [63] , [64] . How about the segment plant RNA viruses and satellites?…”

“…Recent studies have revealed that low CpG and UpA dinucleotide frequencies in animal RNA viruses could avoid specific host defences [99] , [100] , [101] . Similarly, UpA and CpG were largely underrepresented in the genomes of rice stripe virus [65] , potato virus X [102] , SCMV [59] and other potyvirids [66] ( Fig. 3 B).…”

“…Recently, CpG and UpA dinucleotide motifs have been found to be markedly underrepresented in RNA viruses, including plant RNA viruses [39] , [40] , [59] , [65] , [66] . The avoidance of CpG dinucleotide was observed in several potyviruses and other plant RNA viruses [39] , [40] , [59] , [65] , [66] , possibly due to the outcome of selection on nucleotide composition.…”

“…Recently, CpG and UpA dinucleotide motifs have been found to be markedly underrepresented in RNA viruses, including plant RNA viruses [39] , [40] , [59] , [65] , [66] . The avoidance of CpG dinucleotide was observed in several potyviruses and other plant RNA viruses [39] , [40] , [59] , [65] , [66] , possibly due to the outcome of selection on nucleotide composition. Moreover, using PVY as a model, Ibrahim et al (2019) indicated that increased CpG dinucleotide frequencies in the PVY genome showed a reduction in systemic spread and pathogenicity and attenuated replication kinetics in tobacco plants [109] .…”

“…Gaunt and Digard (2021) reviewed the compositional biases mainly in RNA viruses in terms of the causes, consequences and applications [28] . For plant RNA viruses, several recent studies have reported nucleotide composition, codon usage bias, dinucleotide bias and host or vector adaptation [32] , [39] , [40] , [54] , [55] , [56] , [57] , [58] , [59] , [60] , [61] , [62] , [63] , [64] , [65] . In this review, we summarize evolution and host adaptation in plant RNA viral genomes by considering the compositional biases, and widely used software packages for compositional bias analyses.…”