scholarly journals Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

2018 ◽  
Vol 19 (8) ◽  
pp. 2397 ◽  
Author(s):  
Xu Zhang ◽  
Yuchen Cai ◽  
Xiaofeng Zhai ◽  
Jie Liu ◽  
Wen Zhao ◽  
...  
Keyword(s):  
Codon Usage ◽  
Rabies Virus ◽  
Driving Force ◽  
Control Strategies ◽  
Comprehensive Analysis ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Effective Number ◽  
Usage Patterns ◽  
Effective Number Of Codons

Rabies virus (RABV) and other lyssaviruses can cause rabies and rabies-like diseases, which are a persistent public health threat to humans and other mammals. Lyssaviruses exhibit distinct characteristics in terms of geographical distribution and host specificity, indicative of a long-standing diversification to adapt to the environment. However, the evolutionary diversity of lyssaviruses, in terms of codon usage, is still unclear. We found that RABV has the lowest codon usage bias among lyssaviruses strains, evidenced by its high mean effective number of codons (ENC) (53.84 ± 0.35). Moreover, natural selection is the driving force in shaping the codon usage pattern of these strains. In summary, our study sheds light on the codon usage patterns of lyssaviruses, which can aid in the development of control strategies and experimental research.

scholarly journals Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1087 ◽  
Author(s):  
Sheng-Lin Shi ◽  
Run-Xi Xia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Effective Number ◽  
Bias Analysis ◽  
The Family ◽  
Usage Patterns ◽  
Codon Positions ◽  
Effective Number Of Codons

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

Expression levels and codon usage patterns in nuclear genes of the filarial nematodeWucheraria bancroftiand the blood flukeSchistosoma haematobium

2016 ◽  
Vol 91 (1) ◽  
pp. 72-79 ◽  
Author(s):  
G.A. Mazumder ◽  
A. Uddin ◽  
S. Chakraborty
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Evolutionary Relationship ◽  
Nuclear Genes ◽  
Codon Usage Pattern ◽  
Minor Role ◽  
Usage Pattern ◽  
Genetic Characteristics ◽  
Wide Range ◽  
Usage Patterns

AbstractSynonymous codons are used with different frequencies, a phenomenon known as codon bias, which exists in many genomes and is mainly resolute by mutation and selection. To elucidate the genetic characteristics and evolutionary relationship ofWucheraria bancroftiandSchistosoma haematobiumwe examined the pattern of synonymous codon usage in nuclear genes of both the species. The mean overall GC contents ofW. bancroftiandS. haematobiumwere 43.41 and 36.37%, respectively, which suggests that genes in both the species were AT rich. The value of the High Effective Number of Codons in both species suggests that codon usage bias was weak. Both species had a wide range of P3 distribution in the neutrality plot, with a significant correlation between P12 and P3. The codons were closer to the axes in correspondence analysis, suggesting that mutation pressure influenced the codon usage pattern in these species. We have identified the more frequently used codons in these species, most codons ending with an A or T. The nucleotides A/T and C/G were not proportionally used at the third position of codons, which reveals that natural selection might influence the codon usage patterns. The regression equation of P12 on P3 suggests that natural selection might have played a major role, while mutational pressure played a minor role in codon usage pattern in both species. These results form the basis of exploring the evolutionary mechanisms and the heterologous expression of medically important proteins ofW. bancroftiandS. haematobium.

scholarly journals Comprehensive analysis of codon usage pattern of whole genome in protozoa, Stylonychia lemnae

2019 ◽  
Author(s):  
ying wang ◽  
Lin Yao ◽  
Jinfeng Fan ◽  
Xueying Zhang ◽  
Changhong Guo ◽  
...  
Keyword(s):  
Codon Usage ◽  
Classical Model ◽  
Mrna Translation ◽  
Codon Usage Pattern ◽  
Translational Efficiency ◽  
Usage Pattern ◽  
Evolutionary Origins ◽  
Plot Analysis ◽  
Two Factors ◽  
Usage Patterns

Abstract Background: Codon usage pattern is an important evolutionary feature in genomes widely observed in many organisms. Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a germline micronucleus and a vegetative macronucleus. Analysis of codon usage pattern of S. lemnae macronucleus genome helps in understanding evolution at molecular level and acquires significance in mRNA translation, design of transgenic and new gene discovery. Results: The codons of the macronucleus genome sequence of S. lemnae were analyzed and 20,750 coding sequences (CDS) were screened. The overall codon usage of S. lemnae is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in S. lemnae is relatively high. Nucleotide analysis showed that the overall codon usage is biased toward A- and U-ending codons. The phylogenetic analysis indicated that ciliate is independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of S. lemnae is more similar to that of Thtrahymana thermophila and Paramecium caudatum . Correlation analysis, ENC-GC 3S plot, and PR2 plot indicated that the codon usage patterns of S. lemnae are influenced by both mutational pressure and natural selection, neutrality plot analysis showed that those two factors play major roles. C onclusions : Codon usage patterns in eukaryotes are not determined by translational efficiency, but also are determined by the genome. Our study is the first attempt to evaluate the codon usage pattern of S.lemnae macronucleus genome to better understand the evolutionary changes. These results built the base for further research on the molecular evolution of S. lemnae .

scholarly journals The codon usage pattern of the novel coronavirus is drastically different from those of other pathogenic viruses

2020 ◽  
Author(s):  
Xiaolong Wang
Keyword(s):  
Codon Usage ◽  
World Health ◽  
Codon Usage Pattern ◽  
The Novel ◽  
Usage Pattern ◽  
Intermediate Hosts ◽  
Usage Patterns ◽  
Pathogenic Viruses ◽  
Novel Coronavirus ◽  
Health Organization

Abstract The current outbreak of a novel coronavirus (COVID-19) has caused thousands of deaths and has been declared to be a worldwide pandemic by the World Health Organization. There have been various disputes but the origin of COVID-19 is not clear. Here we analyzed the similarities of codon usage patterns between humans and pathogenic viruses, such as human immunodeficiency virus (HIV), highly pathogenic avian influenza (HPAI), SARS, MERS, and COVID-19. In HIVs, HPAIs, SARS, and MERS, codon usages are highly similar to that of humans; in contrast, the codon usage pattern of COVID-19 is drastically different from those of humans and other pathogenic viruses. Besides, coronaviruses have been evolving in two opposite directions: human-preferred codons are adopted to substitute less-preferred ones in SARS and MERS but are substituted by less-preferred ones in COVID-19. The unique codon usage pattern suggesting that COVID-19 was evolved in an intermediate host, in which its codon usage pattern becomes drastically different from that of bats or humans, and its pathogenicity is weakened compared with SARS ad MERS COVs. Finally, we appeal to international cooperation to eliminate the epidemic by cutting off the transmission routes among humans and to search for the origin and intermediate hosts of the novel coronavirus to prevent future animal-to-human transmission.

Characterization of Codon Usage Bias in the UL55 Gene of Duck Enteritis Virus

2011 ◽  
Vol 204-210 ◽  
pp. 649-662 ◽  
Author(s):  
Ying Wu ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Yue Chen
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Duck Enteritis Virus ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
E Coli ◽  
Usage Patterns ◽  
Enteritis Virus

The analysis of codon usage may improve our understanding of the evolution and pathogenesis of DEV（Duck enteritis virus） and allow reengineering of target gene to improve their expression for gene therapy.In this study,we calculated the codon usage bias in DEV UL55 gene and performed a comparative analysis of synonymous codon usage patterns in other 26 related viruses by EMBOSS CUSP program and Codon W on line.Moreover,statistical methods were used to investigate the correlations of these related parameters. By comparing synonymous codon usage patterns in different viruses,we observed that synonymous codon usage pattern in these virus is virus specific and phylogenetically conserved, with a strong bias towards the codons with A and T at the third codon position. Phylogenetic analysis based on codon usage pattern suggested that DEV UL55 gene was clustered with the avian Alphaherpesvirus but diverged to form a single branch. The Neutrality-plot suggested GC12 and GC3s adopt the same mutation pattern,meanwhile,the ENC-plot revealed that the genetic heterogeneity in UL55 genes is constrained by the G+C content, while translational selection and gene length have no or micro effect on the variations of synonymous codon usage in these virus genes.Furthermore, we compared the codon preferences of DEV with those of E. coli, yeast and Homo sapiens.Data suggested the eukaryotes system such as human system may be more suitable for the expression of DEV UL55 gene in vitro. If the yeast and E. coli expression system are wanted for the expression of DEV UL55 gene ,codon optimization of the DEV UL55 gene may be required.

scholarly journals Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin

2020 ◽  
Author(s):  
Kanika Bansal ◽  
Prabhu B. Patil
Keyword(s):  
Amino Acids ◽  
Codon Usage ◽  
Driving Force ◽  
Codon Usage Pattern ◽  
Membrane Glycoprotein ◽  
Usage Pattern ◽  
Systematic Analysis ◽  
Host Jump ◽  
High Degree ◽  
Encoding Genes

AbstractViruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is a driving force in its evolution. Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. At the same time, our analysis suggests that dogs are not a source of SARS-CoV-2. Interestingly, CUP of rdrp displays conservation with two bat SARS isolates RaTG13 and RmYN02. CUP of the SARS-CoV-2 E gene is also conserved with bat and pangolin isolates with variations for a few amino acids. This suggests role allele replacement in these two genes involving SARS strains of least two hosts. At the same time, a relatively conserved CUP pattern in replicase and envelope across hosts suggests them it to be an ideal target in antiviral development for SARS-CoV-2.

scholarly journals Comprehensive analysis of codon usage pattern of whole genome in protozoa, Stylonychia lemnae

2019 ◽  
Author(s):  
Ying Wang ◽  
Lin Yao ◽  
Jinfeng Fan ◽  
Xueying Zhang ◽  
Changhong Guo ◽  
...  
Keyword(s):  
Codon Usage ◽  
Classical Model ◽  
Mrna Translation ◽  
Codon Usage Pattern ◽  
Translational Efficiency ◽  
Usage Pattern ◽  
Evolutionary Origins ◽  
Plot Analysis ◽  
Evolutionary Changes ◽  
Usage Patterns

Abstract Background: Codon usage pattern is an important evolutionary feature in genomes widely observed in many organisms. Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a germline micronucleus and a vegetative macronucleus. Analysis of codon usage pattern of S. lemnae macronucleus genome helps in understanding evolution at molecular level and acquires significance in mRNA translation, design of transgenic and new gene discovery. Results: The codons of the macronucleus genome sequence of S. lemnae were analyzed and 20,750 coding sequences (CDS) were screened. The overall codon usage of S. lemnae is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in S. lemnae is relatively high. Nucleotide analysis showed that the overall codon usage is biased toward A- and U-ending codons. The phylogenetic analysis indicated that ciliate is independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of S. lemnae is more similar to that of Thtrahymana thermophila and Paramecium caudatum . Correlation analysis, ENC-GC 3S plot, and PR2 plot indicated that the codon usage patterns of S. lemnae are not only influenced by mutational pressure but also by natural selection, but neutrality plot analysis showed that the latter plays a major role. C onclusions : Codon usage patterns in eukaryotes are not determined by translational efficiency, but also are determined by the genome. Our study is the first attempt to evaluate the codon usage pattern of S.lemnae macronucleus genome to better understand the evolutionary changes. These results built the base for further research on the molecular evolution of S. lemnae .

Synonymous codon usage pattern in glycoprotein gene of rabies virus

Gene ◽  
2016 ◽  
Vol 584 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Sudhir Morla ◽  
Aditi Makhija ◽  
Sachin Kumar
Keyword(s):  
Codon Usage ◽  
Rabies Virus ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Glycoprotein Gene

scholarly journals Genome-wide characterization and identification of synonymous codon usage patterns in Plasmodium knowlesi

2021 ◽  
Author(s):  
Manoj Kumar Yadav ◽  
Shivani Gajbhiye
Keyword(s):  
Codon Usage ◽  
Plasmodium Knowlesi ◽  
Sequence Data ◽  
Synonymous Codon ◽  
Gc Content ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Optimal Codons ◽  
Usage Patterns

AbstractCodon usage bias is a ubiquitous phenomenon occurring at both, interspecies and intraspecies level in different organisms. P. knowlesi, whose natural host is long-tailed Macaque monkeys, has recently started infecting humans as well. The genome as well as coding sequence data of P. knowlesi is used to understand their codon usage pattern in the light of other human infecting Plasmodium species: P. vivax and P. falciparum. The different codon usage indicators: GC content, relative synonymous codon usage, effective number of codon and codon adaptation index are studied to analyze codon usage in the Plasmodium species. The codon usage pattern is found to be less conserved in studied Plasmodium species, and changes species to species at the genus level. The codon usage pattern of P. knowlesi shows similarity to P. vivax as compared to P. falciparum. The ENC vs. GC3 study indicates that compositional constraints and translation selection is the decisive forces responsible for shaping their codon usage. The studies Plasmodium species shows a higher usage of A/T ending optimal codons. This favors the codon bias in P. knowlesi and P. vivax is due to high selection pressure and in P. falciparum, the compositional mutational pressure is a dominant force. In a nutshell, our finding suggests that the more or less similar codon usage pattern of P. knowlesi and P. vivax may suggest the similar host invasion and immune evasion strategies for disease establishment.

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