Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Abstract

Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses' phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.

Keywords: codon usage bias; narcissus; natural selection; potyviruses.

Figure 1

The Chinese narcissus plants are infected with potyviruses. (A) The potyviruses-infected narcissus plants in Yangzhou city of Jiangsu province, China; (B) Leaves of the Chinese narcissus plants showing mosaic and chlorotic stripes symptoms.

Figure 2

Maximum-likelihood tree was calculated from the coat protein gene sequences of the narcissus yellow stripe virus (A); narcissus degeneration virus (B) and narcissus late season yellows virus (C). Numbers at each node indicate the percentage of supporting bootstrap samples in maximum-likelihood trees. Isolates with red color are determined here.

Figure 2

Maximum-likelihood tree was calculated from the coat protein gene sequences of the narcissus yellow stripe virus (A); narcissus degeneration virus (B) and narcissus late season yellows virus (C). Numbers at each node indicate the percentage of supporting bootstrap samples in maximum-likelihood trees. Isolates with red color are determined here.

Figure 3

The relative and cumulative inertia of the 40 axes from a principal component analysis (PCA) of the relative synonymous codon usage (RSCU) values based on the narcissus yellow stripe virus (A); narcissus degeneration virus (B) and narcissus late season yellows virus (C) CP sequences. The relative (orange bars) and cumulative plot (blue squares) show 40 factors from a principal component.

Figure 4

Correspondence analysis of synonymous codon usage towards the codons in narcissus yellow stripe virus (A); narcissus degeneration virus (B) and narcissus late season yellows virus (C) CP sequences. The analysis is based on the relative synonymous codon usage (RSCU) values of 59 synonymous codons. Different groups are represented by different colors. Among them, NYSV and NLSYV are divided into five groups (Group Ⅰ, Ⅱ, Ⅲ, Ⅳ, Ⅴ), which are represented by dark green, orange, purple, dark red and light green, respectively. NDV is divided into three groups (Group Ⅰ, Ⅱ, Ⅲ) with dark green, orange and purple, respectively.

Figure 5

Effective Number of Codons (ENC) analysis of narcissus yellow stripe virus (A), narcissus de-generation virus (B) and narcissus late season yellows virus (C) coding sequences against GC3s. Effective Number of Codons (ENC) analysis of each coding sequence against GC3s. ENC is the number of effective codons. GC3s nucleotide is the frequency of G + C at the third position of the synonymous codon. The yellow curve (standard curve) shows the relationship between ENC values and GC3s under the random codon usage assumption. Different groups are marked with different colors. Among them, narcissus yellow stripe virus and narcissus late season yellows virus are divided into five groups (Group Ⅰ, Ⅱ, Ⅲ, Ⅳ, Ⅴ) which are represented by red, blue, yellow, green and purple, respectively. Narcissus degeneration virus is divided into three groups (Group Ⅰ, Ⅱ, Ⅲ), which are represented by red, blue, and yellow. The panel on the right graph corresponds to the left graph ABC’s enlarged detailed data graph.

Figure 6

Neutrality plot analysis of the CP genes of narcissus yellow stripe virus (A); narcissus degeneration virus (B) and narcissus late season yellows virus (C) is shown. The abscissa and ordinate are GC3 and GC12, respectively. A value of 0.5 on the abscissa and ordinate indicates that the GC12 usage rate is equal to GC3. Different groups are marked with different colors.

Figure 7

The AU (A3%/ (A3% + U3%)) and GC (G3%/ (G3% + C3%)) bias of the CP genes of narcissus yellow stripe virus (A); narcissus degeneration virus (B) and narcissus late season yellows virus (C) is shown. The center of the plot (both of the coordinates are 0.5) indicates a position where there is no bias. Group Ⅰ, Ⅱ, Ⅲ, Ⅳ and Ⅴ are represented by red, blue, green, purple and yellow dots, respectively.