High codon adaptation in citrus tristeza virus to its citrus host

Abstract

Background: Citrus tristeza virus (CTV), a member of the genus Closterovirus within the family Closteroviridae, is the causal agent of citrus tristeza disease. Previous studies revealed that the negative selection, RNA recombination and gene flow were the most important forces that drove CTV evolution. However, the CTV codon usage was not studied and thus its role in CTV evolution remains unknown.

Results: A detailed comparative analysis of CTV codon usage pattern was done in this study. Results of the study show that although in general CTV does not have a high degree of codon usage bias, the codon usage of CTV has a high level of resemblance to its host codon usage. In addition, our data indicate that the codon usage resemblance is only observed for the woody plant-infecting closteroviruses but not the closteroviruses infecting the herbaceous host plants, suggesting the existence of different virus-host interactions between the herbaceous plant-infecting and woody plant-infecting closteroviruses.

Conclusion: Based on the results, we suggest that in addition to RNA recombination, negative selection and gene flow, host plant codon usage selection can also affect CTV evolution.

Figure 1

N_C-plot of N_Cvalues versus (G + C)₃ contents of CTV isolates. Blue curve indicates the expected curve when all codons are used randomly (no selection) and is calculated using the formula reported by Wright previously [39].

Figure 2

Comparative analysis of nucleotide composition and codon abundance of CTV andC. sinensis. (A) Frequencies of 4 nucleotides at the three positions within a codon for the full CTV coding region (up panel) and coding region of C. sinensis (lower panel). (B) Correlation of the codon abundances between CTV and C. sinensis.

Figure 3

Codon usage variations of CTV genotypes. (A) NJ phylogenetic tree of CTV constructed using the entire coding region. The yellowing and stem-pitting CTV group is colored in blue, the trifoliate orange resistance breaking CTV group is colored in purple, and the quick declining CTV group is colored in yellow. (B) Distributions of CTV codon usage variation along the first and second axes based on the COA analysis. Coordinates of the three CTV groups are colored in the same way as that shown in Figure 3A.

Figure 4

Correlations of the codon abundances of closteroviruses and their respective host species. (A) Beet yellows virus (BYV) versus Beta vulgaris (beet); (B) Carrot yellow leaf virus (CYLV) versus Daucus carrot (carrot); (C) Grapevine rootstock stem lesion associated virus (GRSLaV) versus Vitis vinifera (grapevine); (D) Grapevine leafroll-associated virus 2 (GRLaV-2) versus V. vinifera. The codon usage patterns of beet, carrot and grapevine were downloaded from the Codon Usage Database (http://www.kazusa.or.jp/codon/).