Coronaviruses are enveloped single-stranded RNA genome viruses causing respiratory distress syndromes. The aim of this study was to compare Codon usage, rare Codon clusters and phylogenetic relations in orf1a polyprotein of COVID-19, SARS, and MERS coronaviruses. The frequency, number and fraction of 61 Codons for each amino acid was evaluated in the structure of viral protein and the preferred Codons were assessed using Gene Infinity website. The variations in Codon usage bias were quantified by the ENC and CBI in the ACUA software. Finally, evolutionary relationship and phylogenetic analysis of Coronaviridae were studied using the MEGA 7 software. The GC3% of the cds was in the range from 15.668 to 16.534 and GC3 Skewness from 0.299 to 0.34. Analysis of Codon usage for all of amino acid in SARS, MERS and COVID-19 showed considerable differences between three viruses. The close proximity of COVID-19 and SARS in the tree diagram represented a similarity in their gene sequence of orf1a polyprotein (pp1a). This phylogenetic analysis also indicated that COVID-19 and SARS had the near phylogenetic relation based on the nucleotide sequences of orf1a polyprotein in comparison to MERS. The findings of the present study revealed that the patterns of base compositions in COVID-19 are most likely the result of mutation pressure rather than that of natural selection, since at all Codon positions its effects are present. In addition, analysis of base composition it was found that the cds of COVID-19 are rich in AT, which should be considered in designing new drugs.

The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) initially appeared as part of an important prevalence of respiratory disease centered in Hubei province, China. Now, it is a pandemic globally and is a significant public health concern. Taxonomically, SARS-CoV-2 was revealed to be a Beta coronavirus (lineage B) related to SARS-CoV and SARS-related bat coronaviruses closely, and it has been stated to have a similar receptor with SARS-CoV (ACE-2). Here, we carried out the Codon usage bias (CUB) by analyzing the Codon bias index (CBI), Codon adaptation index (CAI), and an effective number of Codons (ENC) besides phylogenetic analysis of Coronaviridae and also structural modeling of the SARS-CoV-2 spike glycoprotein. We observed that 2019-nCoV has a rich composition of AT nucleotides that strongly affects its Codon usage, which seems to be not optimized for the human hosts. Moreover, a close evolutionary phylogenetic relationship was detected between SARS-CoV-2/human/IRIN/ and SARS-CoV-2/human/CHN/WH-09/2020. By in silico modeling of spike glycoprotein, an I-TASSER server, the 3Dstructure of it was also evaluated. This type of analysis would be beneficial for exploring a virus adaptation to host, and evolution and is therefore of value to developing vaccine design and pharmaceutical agents.

Background: Most of the amino acids are encoded by more than one Codon, termed as synonymous Codons. Synonymous Codon usage is not random as it is unique to species. In each amino acid family, some synonymous Codons are preferred and this is referred to as synonymous Codon usage bias (SCUB). Trends associated with evolution of SCUB and factors influencing its diversification in plastomes of genetically distinct Oenothera plastomes have not been investigated so far.Objectives: In the present study, major forces that shape SCUB in Oenothera plastomes and putative preferred Codons in the protein coding genes (PCG) of plastomes were identified.Materials and Methods: To unravel various features of SCUB across selected Oenothera plastomes, commonly used Codon usage indices such as relative synonymous Codon usage (RSCU), synonymous Codon usage order (SCUO), effective number of Codons (ENC) and Codon adaptation index (CAI) were calculated. Correspondence analysis (COA) on RSCU was performed to identify various characteristics of SCUB across different PCG in Oenothera plastomes. Spearman’s rank correlation analysis was adopted to correlate nucleotide contents, Codon usage indices and major axes of COA to find out critical parameters in shaping SCUB.Results: Mutational bias due to compositional constraints played crucial role in shaping SCUB as T3 and GC3 contents were in strong negative correlation with all axes of COA. Nevertheless, significant negative correlations between axis 1 and 3 with ENC and CAI respectively, in all species, and narrow distribution of GC contents in neutrality plot, indicate the role of natural selection. Hydropathy score of proteins was found to be influencing SCUB in O. glazioviana as it showed strong negative correlation with axis 2.Conclusion: We concluded that mutational pressure coupled with weak selection influenced SCUB in the examined plastomes of Oenothera. In addition, all examined species of Oenothera exist as disjunct populations in different parts of North America and these populations might have experienced genetic drift as random mutations in small populations that have been fixed over a period of time.

Today, cows are selected using genetic information at the level of the genome translation, transcriptome and proteome. In this regard, there is a high correlation between Codon usage patterns at the genome level and the level of expression of genes in the genome level, which are related to the expression and translation of the genes, this indicator is the result of a balance between factors such as mutation, natural selection, GC content and gene expression level. This information is useful in evaluating the evolutionary process and changes in the genome and predicting gene expression levels within species. However, there is limited information on the study of Codon usage in bulls. In the present study, the Codon usage pattern between two Holstein )Bos Taurus(and cholistani)Bos indicus(cattle populations is evaluated using gene expression data with different expression and its relation with gene expression. For this purpose, in this study, RNA-Seq data were used to assemble 40 samples of Holstein)Bos Taurus) and 45 cholistani (Bos indicus) breeds. Finally, the Codon usage pattern was calculated based on indices such as ENC, GC3S, CAI and GC for different expression genes between the two breeds using the Codon W software. Also, R 3. 4. 2 Statistical software was used to calculate the correlation between the desired indicators and the graphs. An analysis of Codon usage for ORF regions with different expressions in both Holstein and cholistani breeds showed that there is a high correlation between the total GC and GC3S values, which indicates the effect of GC and mutation as an important factor in the creation of various Codons; Also, the correlation between ENC and GC3S showed that mutation was the most important factor in the formation of Codons. The correlation between the CAI indexes, which is mainly used to predict gene expression levels, with the ENC index indicates the association between the Codon usage pattern and the gene expression. This is the first report to examine the Codon biology between the two Holstein and cholistani breeds, which not only provide a new perspective for understanding the mechanisms of the Codon preference model, but also provide useful clues for molecular genetics and evolutionary studies.

In order to study and compare the phosphate transporter gene Codon usage and it's respond to the traits like salt tolerance, day length, Pollination and temperature in different plants, 100 isoform from 10 plants are extracted from NCBI website and then analyzed with Gene Infinity and Minitab 16 software. The result shows that the highest Codon usage similarity (81.95%) was for wheat and oryza (annual, self-polinated and Psychrophilic) from Poaceae family. The result for poaceae family shows that the highest mean abundance was for Codons that have U or G at the end. In this study Cucurbita maxima (salt tolerance, annual and cross pollinated) have the lowest Codon usage similarity (70.37%) in compare with other plants in this study. The highest difference between families was for Fabaceae (77.64%) but they are divided in one group at the cluster. So the results show that the families that have lowest distance have the highest Codon usage similarity in terms of salt tolerance, day length, Pollination and temperature. It is conceivable that a direct relationship would exist between preferred Codons and division of plant families.

Objective: The production of heterologous proteins in Escherichia coli is strongly affected by Codon bias. This phenomenon occurs when the Codon usage of mRNA coding for the foreign protein differs from that of the bacterium. The ribosome pauses upon encountering a rare Codon and may detach from mRNA, thereby the yield of recombinant protein production reduces. The aim of this study is to investigate the effect of these Codon numbers reductions on the recombinant protein production.Materials and Methods: Since most amino acids are encoded by more than one Codon, Codons were changed in order to their usage in a special host such as E. coli without any transformation in amino acids sequence. Silent mutations in 5' Codons of human basic fibroblast growth factor cDNA carried out by site-directed mutagenesis and the expression level of the recombinant protein is analyzed by means of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot.Results: Expression level in mutant and wild-type genes indicated a considerable difference. In contrast with the remarkable bands of wild-type gene in all the strains particularly in Codon plus strain, there were no significant bands related to mutant gene in SDS-PAGE analysis. Conclusion: Because of the same conditions of mutant and wild-type genes during the translation and transcription, this significant difference may relate to mRNA efficiency for translation. Our results indicate that increased stability of 5' mRNA secondary structures in E. coli prevents efficient translation initiation. Furthermore, wild-type gene significant bands in Codon plus strain support the hypothesis that the possible elimination of translational pauses that increase translation rate leads to over expression.