The analyses of relationships among nucleotide, synonymous codon and amino acid usages for E2 gene of bovine viral diarrhea virus

Ma, Xiaoxia; Ma, Peilin; Chang, Qiu-yan; Li, Linjie; Zhou, Xiao-kai; Zhang, Derong; Li, Mingsheng; Cao, Xin; Ma, Zhiyong

doi:10.1016/j.gene.2018.03.065

Cited by 5 publications

(4 citation statements)

References 33 publications

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“…Generally, the higher the ENC value, the lower the codon usage bias. For the E2 gene of APPV, ENC values ranged from 49.15 to 61.00, and the mean value of ENC was 52.74 ± 2.69, which was higher than that in other members of pestivirus, including CSFV (52.33) and BVDV (51.43) (Chen et al 2017;Ma et al 2018). It is worth note that the ENC value of one Chinese APPV strain even reached to maximum, which suggested that no codon usage Fig.…”

Section: Discussionmentioning

confidence: 88%

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Liu

et al. 2021

Biochem Genet

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Atypical porcine pestivirus (APPV) is an emerging novel pestivirus causing the congenital tremor (CT) in piglets. The worldwide distribution characteristic of APPV make it a threat to global swine health. E2 is the major envelope glycoprotein of APPV and the crucial target for vaccine development. Considering the genetic variability of APPV complete genomes and its E2 gene as well as gaps for codon analysis, a comprehensive analysis of codon usage patterns was performed. Relative synonymous codon usage (RSCU) and effective number of codon (ENC) analyses showed that a relatively instable change existed and a slight low codon usage bias (CUB) were displayed in APPV genomes. ENC-plot analysis and correlation analyses of nucleotide compositions and ENC showed that mutation pressure and natural selection both affected the codon usage bias of the APPV and natural selection had a more obvious influence for E2 gene compared with complete genomes. Principal component analysis (PCA) and correlation analyses confirmed the above results. Correlation analyses between Gravy and Aromaticity values and the codon bias showed that natural selection played an important role in shaping the synonymous codon bias. Furthermore, neutrality plot analysis showed that natural selection was the main force while mutation pressure was a minor force influencing the codon usage pattern of the APPV E2 gene and complete genomes. The results could illustrate the codon usage patterns of APPV genomes and provided valuable basic data for further fundamental research of evolution of APPV.

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Section: Discussionmentioning

confidence: 88%

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Liu

et al. 2021

Biochem Genet

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“…Although mutation pressure derived from nucleotide usages was identified as the dominant evolutionary dynamic in genomes of Chlamydia spp., other evolutionary dynamics, such as natural selection, also influenced codon usage patterns to modify the evolutionary trends of Chlamydia spp. In previous reports, GC3 content was regarded as a ruler, which is often used for reflecting influences of the overall nucleotide composition variations on codon usages at gene levels [31,40,41,42,43]. The four nucleotide bases are regarded as footstones for genomic organization of microorganisms, the systemic and general estimation of four nucleotide usage patterns is better than the estimation of GC3 content or AT3 content when displaying the roles of nucleotide usage patterns in formation of synonymous codon usage patterns [44,45].…”

Section: Discussionmentioning

confidence: 99%

Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

Cao

et al. 2018

IJMS

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The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

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“…A synonymous codon is redundant and most amino acids are encoded by more than one synonymous codon. The synonymous codon usage pattern is crucial in modulating the efficiency and accuracy of viral protein translation and maintaining the viral protein amino acid sequence [11][12][13]. Synonymous codon usages in the viral genome can reflect the active cross-talk between viral infection and host immune response [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts

et al. 2022

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Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via V s calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (V s value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (V s < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (V s > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.

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The analyses of relationships among nucleotide, synonymous codon and amino acid usages for E2 gene of bovine viral diarrhea virus

Cited by 5 publications

References 33 publications

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts

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