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Original Articles

Evolution of codon usage in Zika virus genomes is host and vector specific

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Pages 1-14 | Received 01 Jul 2016, Accepted 25 Aug 2016, Published online: 25 Jan 2019

Figures & data

Figure 1 Genotype-specific comparative analysis of ENC values of ZIKV coding sequences.

Table 1 The relative synonymous codon usage (RSCU) patterns of ZIKV, its host and transmission vectors

Figure 2 Correspondence analysis (CA). Genotype-specific CA plots were constructed for whole genome and individual ZIKV coding sequences. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A. The ZIKV strain isolated from Ae. aegypti is represented as a black color diamond.

Figure 3 ENC–GC3 plots. The curve indicates the expected codon usage if GC compositional constraints alone account for the codon usage bias. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A.

Figure 4 CAI analysis of the ZIKV coding sequences in relation to its host and vectors. East African, EA; west African, WA.

Figure 5 RCDI analysis of the ZIKV coding sequences in relation to its host and vectors. East African, EA; west African, WA.

Figure 6 SiD analysis of ZIKV strains in relation to its host and vectors. (A) Whole genome. (B) C. (C) prM. (D) E. (E) NS1. (F) NS2A. (G) NS2B. (H) NS3. (I) NS4A. (J) NS4B. (K) NS5. The description of color coding is same as that of A.

Supplemental material

Supplementary Figure S1.

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Supplementary Figure S2.

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Supplementary Figure S3.

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Supplementary Table S1.

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Supplementary Table S2.

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Supplementary Table S3.

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Supplementary Table S4.

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Supplementary Table S5.

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