Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Abstract

Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.

Genome-wide analysis of codon usage bias in four sequenced cotton species

“…Studies have shown that the higher the gene expression level is, the stronger is the preferred use of codon [1][2][3]6,15,16,49,[55][56][57][58][59][60]. In our study, the codon usage bias results of all cotton species were shown in S1 Table. The correlation between the parameters of 4 cotton species and 4 subgenomes had the same rule, except the correlation between G3s and C3s.…”

“…GC12 represents the average GC content of the first and second positions of the codons. A significant correlation between GC12 and GC3 values means that mutational stress is superior to translation selection in the formation of codon usage bias while non-significant correlation between them reveal that translation selection plays dominant role in codon usage preference [55,[61][62][63]. In our study, firstly we took the nuclear genome CDSs of each cotton species and subgenome as a whole and calculated one GC12/GC3 value per cotton species to analyze the correlation coefficients between GC12 and GC3 in 4 cotton species and 4 subgenomes.…”

Cross‐species transmission of the newly identified coronavirus 2019‐nCoV

“…Studies of relative synonymous codon usage (RSCU) bias between viruses and their hosts suggested that viruses tends to evolve codon usage bias that is comparable to their hosts. 10,11 Results from our analysis suggest that 2019-nCoV has most similar genetic information with bat coronovirus and has most similar codon usage bias with snake. More interestingly, an origin-unknown homologous recombination may occured within the spike glycoprotein of the 2019-nCoV, 5 which may explain its cross-species transmission, and limited person-person spread.…”

Potential mechanisms of Zika‐linked microcephaly

“…It contains a positive‐strand, RNA genome that encodes a single long open reading frame that is posttranslationally modified to generate structural and nonstructural ZIKV proteins . ZIKV can and has evolved rapidly, with distinct strains isolated from numerous locations throughout the world (Refs ; see also Box ). Structural studies of ZIKV indicate that its protein coat, comprised primarily of envelope (E) protein, is similar to other flaviviruses .…”