Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms

In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms （i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639）. The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the hving environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes.

Analysis of Codon Usage Between Different Poplar Species

Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.

The Factors Shaping Synonymous Codon Usage in the Genome of Burkholderia mallei

Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.

Synonymous codon usage in Methanosarcina mazei str.Goe1 and other Euryarchaeota microorganisms

A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160）. Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms＇ codon usage pattems.

Site discrepancy of synonymous codon usage in SARS coronavirus and other viruses in Coronaviridae

The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.

Analysis of synonymous codon usage in chloroplast genome of Populus alba

The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G＋C in synonymously variable third position of sense codon （GC3S）, （r=0.349）, and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI （r=-0.348, p〈0.01 and r=0.602, p〈0.01）. The ENc for most genes was similar to that for the expected ENc based on the GC3s, but several genes with low ENc values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast gcnome ofP. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome ofP alba.

Patterns of synonymous codon usage bias in chloroplast genomes of seed plants

Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in chloroplast genomes of seed plants. The results show that chloroplast genomes of the six seed plants had similar codon usage patterns, with a strong bias towards a high representation of NNA and NNT codons. In chloroplast genomes of the six seed plants, the effective number of codons （ENC） for most genes was similar to that of the expected ENC based on the GC content at the third codon position, but several genes with low ENC values were laying below the expected curve. All of these data indicate that codon usage was dominated by a mutational bias in chloroplast genomes of seed plants and that selection appeared to be limited to a subset of genes and to only subtly affect codon usage. Meantime, four, six, eight, nine, ten and 12 codons were defined as the optimal codons in chloroplast genomes of the six seed plants.

Genome-wide analysis of the synonymous codon usage patterns in apple

Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS（Statistical Product and Service Solutions） programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.

Synonymous codon usage pattern in model legume Medicago truncatula

Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences （CDSs） from M. truncatula were examined for codon usage bias （CUB）. Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.

Characterization of Synonymous Codon Usage Bias in the Pseudorabies Virus US1 Gene

In the present study, we examined the codon usage bias between pseudorabies virus （PRV） US1 gene and the USl-like genes of 20 reference alphaherpesviruses. Comparative analysis showed noticeable disparities of the synonymous codon usage bias in the 21 alphaherpesviruses, indicated by codon adaptation index, effective number of codons （ENc） and GC3s value. The codon usage pattern of PRV US1 gene was phylogenetically conserved and similar to that of the USl-like genes of the genus Varicellovirus of alphaherpesvirus, with a strong bias towards the codons with C and G at the third codon position. Cluster analysis of codon usage pattern of PRV US1 gene with its reference alphaherpesviruses demonstrated that the codon usage bias of USl-like genes of 21 alphaherpesviruses had a very close relation with their gene functions. ENc-plot revealed that the genetic heterogeneity in PRV US1 gene and the 20 reference alphaherpesviruses was constrained by G＋C content, as well as the gene length. In addition, comparison of codon preferences in the US1 gene of PRV with those ofE. coli, yeast and human revealed that there were 50 codons showing distinct usage differences between PRV and yeast, 49 between PRV and human, but 48 between PRV and E. coil Although there were slightly fewer differences in codon usages between E.coli and PRV, the difference is unlikely to be statistically significant, and experimental studies are necessary to establish the most suitable expression system for PRV US1. In conclusion, these results may improve our understanding of the evolution, pathogenesis and functional studies of PRV, as well as contributing to the area of herpesvirus research or even studies with other viruses.

Analysis of Synonymous Codon Usage Bias in 09H1N1

A novel subtype of influenza A virus 09H1N1 has rapidly spread across the world. Evolutionary analyses of this virus have revealed that 09H1N1 is a triple reassortant of segments from swine, avian and human influenza viruses. In this study, we investigated factors shaping the codon usage bias of 09H1N1 and carried out cluster analysis of 60 strains of influenza A virus from different subtypes based on their codon usage bias. We discovered that more preferentially used codons of 09H1N1 are A-ended or U-ended, and the intra-genomic codon usage bias of 09H1N1 is quite low. Base composition constraint, dinucleotide biases and translational selection are the main factors influencing the codon usage bias of 09H1N1. At the genome level, we find that the codon usage bias of 09H1N1 is similar to H1N1 (A/swine/Kansas/77778/2007H1N1), H9N2 from Asia, H1N2 from Asia and North America and H3N2 from North America. Our results provide insight for understanding the processes governing evolution, regulation of gene expression, and revealing the evolution of 09H1N1.

Factors affecting mito-nuclear codon usage interactions in the OXPHOS system of Drosophila melanogaster

Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.

Analyses on the Overall Codon Usage Pattern in Fish Rhabdovirus

The codon usage bias and the base compositions in the available 49 complete fish rhabdovirus genome sequences were investigated. The high correlation between GC12% and GC3% suggested that mutational pressure rather than natural selection was the main factor determining the codon usage and base component in fish rhabdovirns, most of the spots lying below the expected curve （ ENC vs GC3% ） also suggested that codon usage bias in these 49 genomes was influenced by mutational pressure in codon usage pattern. Through PCA analysis based on RSCU, all ORFs in the 49 fish rhabdoviurs genomes were clustered into two parts, and this result showed that hosts played a role in codon usage pattern of fish rhabdovirns genomes. Further, comparison between SVCV, INHV, VHSV and their hosts suggested the effect of natural host on the codon usage pattern took part in the evolution process of fish rhabdovirns. This study represents the most comprehensive analysis to date for fish rhabdovirus eodon usage patterns.

Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome

Objective In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage,codon usage patterns of chloroplast genome,we determine the complete chloroplast(cp)genome of B.falcatum and clarify the main factors that influence codon usage patterns of 78 genes in B.falcatum chloroplast genome.Methods The total genomic DNA of fresh leaves from a single individual of B.falcatum was extracted with EASYspin plus Total DNA Isolation Kit and 2μg genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform.The cp genome of B.falcatum was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters.Python script and Codon W were used to calculate the codon usage bias parameters.Results The full length of B.falcatum cp genome was 155851 bp,132 different genes were annotated in this cp genome containing 80 protein-coding genes,30 tRNA genes,and four rRNA genes.The codon usage models tended to use A/T-ending codons.The neutrality plot,ENC plot,PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in B.falcatum cp genome.Furthermore,three optimal codons were identified and most of these three optimal codons ended with G/U.Conclusion The cp genome of B.falcatum has been characterized and the codon usage bias in B.falcatum cp genome is influenced by natural selection,mutation pressure and nucleotide composition.The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes,genetic engineering and molecular evolution in B.falcatum.

Comparative Analysis of Codon Usage Patterns Among Mitochondrion, Chloroplast and Nuclear Genes

In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat （Triticum aestivum L.）. GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 （PR2） plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.

Codon Usage Biases of Transposable Elements and Host Nuclear Genes in Arabidopsis thaliana and Oryza sativa

Transposable elements （TEs） are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa （r=0.944 and 0.839, respectively, P〈0.0001） but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species.

Exploring Codon Usage Patterns of Alternatively Spliced Genes in Human Chromosome 1

In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage data analysis indicates that G- and C-ending codons are predominant in the genes. The base usage in all three codon positions suggests a selection-mutation balance. Multivariate statistical analysis reveals that the codon usage variation has a strong positive correlation with the expressivities of the genes (r=0.5790, P<0.0001). All 27 codons identified as optimal are G- and C-ending codons. Correlation analysis shows a strong negative correlation between the gene length and codon adaptation index value (r=0.2252, P<0.0001), and a significantly positive correlation between the gene length and Nc values (r=0.1876, P<0.0001). These results suggest that the comparatively shorter genes in the genes have higher codon usage bias to maximize translational efficiency, and selection may also contribute to the reduction of highly expressed proteins.

Epidemiological Surveillance: Genetic Diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019

Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.

Comparative analysis of flower-meristem-identity gene APETALA2 (AP2) codon in different plant species

The flower-meristem-identity gene APETALA2(AP2), one of class-A genes, is involved in the establishment of the floral meristem and the forming of sepals and petals. Codon usage bias(CUB) identifies differences among species, meanwhile dynamic analysis of base composition can identify the molecular mechanisms and evolutionary relationships of a specific gene. In this study, eight coding sequences(CDS) of AP2 gene were selected from different plant species using the Gen Bank database. Their nucleotide composition(GC content), genetic index, relative synonymous codon usage(RSCU) and relative codon usage bias(RCUB) were calculated with R Software to compare codon bias and base composition dynamics of AP2 gene codon usage patterns in different plant species. The results showed that the usage of AP2 gene codons from different plant species were influened by GC bias, especially GC3 s. Overall, base composition analysis indicated that the usage frequency of codon AT in the gene coding sequence was higher than GC among AP2 gene CDS from different plant species. Furthermore, most AP2 gene CDSs ended with AT; AGA, GCU and UGU had relatively high RSCU values as the most dominant codon; the usage characteristic of the AP2 gene codon in Malus domestica was similar to that of Vitis vinifera; Paeonia lactiflora was similar to Paeonia suffruticosa and Solanum lycopersicum was similar to Petunia×hybrida. There was a moderate preference in the usage of AP2 gene codon among different plant species from relatively low frequency of optimal codon(Fop) values and high effective number of codons(ENC) value. This study has revealed the usage characteristics of the AP2 gene codon from the comparision of AP2 gene codon preference and base dynamics in different plant species and provide a platform for further study towards transgenic engineering and codon optimization.

Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses

The monkeypox virus(mpox virus,MPXV)epidemic in 2022 has posed a significant public health risk.Yet,the evolutionary principles of MPXV remain largely unknown.Here,we examined the evolutionary patterns of protein sequences and codon usage in MPXV.We first demonstrated the signal of positive selection in OPG027,specifically in the CladeⅠlineage of MPXV.Subsequently,we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak.Furthermore,we showed strong epistasis between amino acid substitutions located in different genes.The codon adaptation index(CAI)analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes,and the CAI decreased over time and diverged between clades,with CladeⅠ>Ⅱa andⅡb-A>Ⅱb-B.While the decrease in fatality rate among the three groups aligned with the CAI pattern,it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates.This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.