Codon bias refers to the differences in the frequency of occurrence of synonymous Codons in coding DNA. Pattern of Codon and optimum Codon utilization is significantly different between the lives. This difference is due to the long term function of natural selection and evolution process. Genetics drift, mutation and regulation of gene expression are the main reasons for Codon bias. In this study, the Codon bias analysis was done on photosynthesis and respiratory related genes of phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), pyruvate orthophosphate dikinase (PPDK), glycerate kinase (GK) (nuclear genes), rubisco, NADH-dehydrogenase subunit F and cytochrome-C (chloroplast genes) from Aeluropus littoralis plant. Nuclear gene sequences were obtained after partial isolation and for chloroplast genes obtained from nucleotide database. Calculation of Codon adaptation index (CAI) showed that studied genes with direct or indirect association with photosynthesis, had high level of gene expression and had also a tendency to optimum Codon utilization. The results also showed the difference in Codon bias between genes encoded in nucleus and chloroplast for some amino acids.

The family, Flaviviridae includes viruses which cause several diseases including Dengue fever, Japanese encephalitis, Murray Valley encephalitis, Tick-borne encephalitis, West Nile encephalitis, Yellow fever and Hepatitis C virus infection. Members of this family have monopartite, linear, single-stranded RNA genomes of positive polarity with 9.6-12.3 kb in length. Here, we analyzed the Codon usage of 13 species of this family by using gene infinity package. Base analysis was performed by CAIcal server and amino acid composition was calculated by PseAAC web-server. The results showed that the highest number of A, G and C bases were seen in the RNA genome of Dengue virus 2, Tick borne encephalitis virus and Hepatitis C virus, respectively.Although the number of U bases used in RNA genomes was very close, the highest U nucleotide amount was 23.77% in Wesselsbron virus. The lowest number of C, G, U and A bases was seen in Bovine viral diarrhea virus, Dengue virus 2, Tick borne encephalitis virus and Hepatitis C virus, respectively. In this study, it was found that the complete genome of classical swine fever virus has a lower GC content and genome of Tick borne encephalitis virus, Hepatitis C virus and Powassan virus have the highest GC content among other examined species. We also classified the amino acids as rare (Phenylalanine, Cysteine, Histidine, Methionine, Asparagine, Glutamine, Tryptophan and Tyrosine), frequent (Alanine, Glutamic acid, Glycine, Leucine, Valine and Threonine), and intermediate (all others). The highest numbers of preferred Codons exist in Wesselsbron virus and the lowest in West Nile virus.

Codon usage and rare Codons have mixed results on the protein structure and function. An increasing amount of data is shown that replacing the rare Codons with frequently synonymous ones has diverse results as a decrease in a protein’s specific activity, changing the folding pathway, and reducing protein solubility. In this study, we investigated the situation of Codon usage of the Lampyridae family luciferases using computational databases. For this, the Codon feature of these luciferases was studied, bioinformatically. Also, in silico analyses of this enzyme were conducted by structural modeling on the I-TASSER web server. The status of these rare Codons in these structural models was studied using SPDBV and PyMOL software. Finally, the binding site properties were studied using the AutoDock Vina. Using molecular modeling, two rare Codons (Arg533 and Arg536) were analyzed that may have a critical role in the structure and function of these luciferases. AutoDock Vina was used in molecular docking that recognizes some residues that yield closely related to luciferyl-adenylate binding sites. These analyses created a new understanding of the sequence and structure of these luciferases, and our findings can be used in some fields of clinical and industrial biotechnology. This bioinformatics analysis plays an essential role in the design of new drugs.

Background and Object: Calpastatin (CAST) is one of the enzymes of Calpine proteolytic system. The proteolytic protein complex contains Ca+2 dependent proteases which contributes in construction, degradation and muscle tissue compression after slaughter, and is also regarded a candidate gene associated with growth efficacy and quality of meat. Materials and Methods: In this study, gene and protein coding sequences region of CAST in six mammalian species (human, rat, cattle, yak, sheep and goat) were examined. Gene and protein sequences were retrieved from gene bank and then analyzed. Homology analysis and alignment, phylogenetic and nucleotide diversity and variation in coding region and stop Codon were carried out using the Clustal Ω and Mega7 softwares. SOPMA and Protparam programs were used for homology and alignment analyses, and to investigate the atoms diversity in protein structure, amino acid and terminal amino acid diversity in sequences retrieved from the NCBI database. Preferred Codon sequences were obtained using CodonW software to explore the Codon usage locus. Results: Codon adaptation index (CAI) had the highest value for yak (0. 256) and lowest value for sheep (0. 236). Analysis by bioinformatic software for better understanding of protein structure of CAST showed that, in all sequences, lysine amino acid was the most frequent by 623 observations and tryptophan was the least with 5 repeats in the structure of the protein. The ration of Polar amino acids to non-polar amino acids in the protein was 2. The relative efficiency of synonymous Codons (RSCU) for the amino acids serine and aspartic acid as the terminal amino acid in different species were, respectively, (AGC =1/38) and (GAU =1/01). Ovisaries species showed the maximum PI and Capra hircus species had the highest value of effective number of Codons index (ENC). Conclusion: hydrophobic amino acids constitute the main part of the amino acid sequence of Calpastatin protein. Given the role of inhibition of Calpastatin protein for the activity of the enzyme Calpain in muscle and considering that the most sequences of Calpain are captured by hydrophilic amino acids, the explore of amino acid sequence in Calpastatin and the role of these hydrophobic amino acids against the hydrophilic amino acids in Calpain is important. Calpastatin protein is much more tolerant in humans than ruminants. The Codon bias analysis of the studied species showed that, in the evolution, Bos grunniens protein species had higher phenotype appearance for preferred Codons than other species and function of the optimal Codons were shown to be stronger than others.

Background and Aims: The genetic variability and population structure of Grapevine leafroll-associated virus 3 (GLRaV-3) have not already been studied in mid-Eurasia Iran. The investigations will contribute to developing efficient and durable control strategies of latent and graft-transmissible virus. Materials and Methods: During the winter of 2018-2019, a total of 229 dormant cutting samples were collected from 15 vineyards in West Azarbaijan province. All the samples were analyzed by serological and RT-PCR assays. The phylogenetic tree and two-dimensional nucleotide diversity plot were constructed using CP sequences by the SplitsTree4 v.4.12.6, and SDTv1.2 soft wares, respectively. Dnasp v.6.10.04 was used for genetic diversity and demographic analysis. We provide analyses of the Codon usage and composition of GLRaV-3 based on 517 nucleotide sequences of the CP gene including 11 full CP sequences from Iran.  Results: Using serological assay 31.87% GLRaV-3 infection was detected. Neighbor-Net method analysis of the virus complete CP gene showed that the Iranian isolates fell into phylogroup I (GI) “as it is dominant in the rest of the world”. High haplotype diversities indicate the recent expansion of GLRaV-3. No clustering was found according to where the GLRaV-3 was isolated. Using dN/dS values it was found that the different populations of this virus is under negative (purifying) selection. The highest gene flow was determined between Europe and East Asia. Moderate or low genetic differentiation, and frequent gene flow (FST < 0.33 and Nm > 1) also confirmed with Ks*, Kst* Z, Z* and Snn statistics values. The frequency of amino acid coded by A/G ended optimal Codon indicates the overlapping influences of natural selection and mutational pressure on the Codon preferences in the CP gene. Codon bias of the CP gene was strongly affected by natural selection rather than mutation according to the effective number of Codons-ENC vs. GC3s plot. Principal component plot analysis (PCA), illustrated the possible origin of GLRaV-3 in the Old World.  Conclusions: This analysis is the first demonstration of the population structuring of GLRaV-3 in mid-Eurasian Iran. Indeed, these consequences explain selectively driven Codon bias in GLRaV-3 species; and reveal the potential importance of expression-mediated selection in shaping the genome evolution of this virus.

Bacground and Objectives: Start Codon is the first Codon that can be translated to amino acid after transcription of mRNA from DNA. In all prokaryotes and eukaryotes the genetic code for start Codon is ATG that will translate to methionine at the beginning of peptide chain via tRNA, rRNA and other parts of protein synthesis machine but a rare exception was recognized in this universal rule. This kind of exception on universal rule of start Codon in eukaryotic genes is important and notable.Materials and Methods: After isolation, cloning and sequencing of phospholipase B2 gene from pathogenic mold Aspergillus fumigatus (afplb2), usual ATG start Codon was not seen at predicted region of obtained sequence and instead of this Codon, GTG Codon was present at predicted position.Results: Control of every possible factor for prevention from any mistake for sequences of afplb2 gene were not leads to any mistake and also triple reading of both strand of afplb2 gene were not shown any misreading on the length of cloned gene. Search in the web and submitted genes sequences at different Gene Banks was shown two similar exception on the sequences of start Codon and replacement of GTG to ATG on glyceraldehde-3-phosphate dehydrogenaseencoding (gpdA) gene from Phytophotora infestans and gene encoding alpha-aminoadipylcysteinyl- valine synthetase (pcbAB) from Cephalosporium acremonium.Conclusion: It seems that a point mutation has been replaced a purine (G) “guanine” with another purine (A) “adenine” and due to point mutation valine amino acid has been replaced with methionine at the beginning of peptide chain.

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.