Analysis of the chloroplast genome of Incarvillea younghusbandii Sprague / 生物工程学报

Incarvillea younghusbandii Sprague is a traditional tonic herb. The roots are used as herbal medicine for nourishing and strengthening, as well as treating postpartum milk deficiency and weakness. In this study, the chloroplast genome of I. younghusbandii was sequenced and assembled by the high-throughput sequencing technology. The sequence characteristics, sequence repeats, codon usage bias, phylogenetic relationships and estimated divergence time of I. younghusbandii were analyzed. The 159 323 bp sequence contained a large single copy (80 197 bp), a small single copy (9 030 bp) and two inverted repeat sequences (35 048 bp). It contained 120 genes, including 77 protein coding genes, 8 ribosomal RNA genes and 35 transfer RNA genes. AAA was the most frequent codon in the chloroplast coding sequence of I. younghusbandii. A total of 42 simple sequence repeats were identified in the chloroplast genome. Phylogenetic analysis revealed I. younghusbandii was mostly like its taxonomically close relative Incarvillea compacta. The divergence between I. younghusbandii and I. compacta was dated to 4.66 million years ago. This study was significant for the scientific conservation and development of resources related to I. compacta. It also provides a basic genetic resource for the subsequent species identification of the genus Incarvillea, and the population genetic diversity study of Bignoniaceae.

Codon usage by chloroplast gene is bias in Hemiptelea davidii

The base composition of the chloroplast genes is of great interest because they play a highly significant role in the evolutionary development of the plants. Evaluation of the 48 chloroplast protein-coding genes of Hemiptelea davidii showed that the average GC content was about 37.32%, while at the third codon base position alone the average GC content was only 27.80%. The 48 genes were classified into five groups based on the gene function and each group displayed specific codon characteristics. Based on the relative synonymous codon usage analysis, a total of 30 high-frequency codons and 11 optimal codons were identified, most of them ended with A or T. Neutrality plot, ENC-plot and PR2-plot analyses showed that the codon usage bias of the chloroplast genes of H. davidii was greatly influenced by natural selection pressures. Meanwhile, the frequency of codon usage of chloroplast genes among different plant species displayed similarities, with some synonymous codons were preferred to be used in H. davidii. In this study, the codon usage pattern of the chloroplast proteincoding genes of H. davidii provides us with a better understanding of the expression of chloroplast genes, and may advice the future molecular breeding programmes.

Analysis of codon usage patterns in Polyporus umbellatus based on transcriptome data / 药学学报

We obtained 332 coding sequences from the Polyporus umbellatus transcriptome based on the BLASTx and ESTScan analyses. The codon usage patterns of P. umbellatus were calculated and statistically analyzed using CodonW. The results showed that the average GC content of genes was 53.57% and the average GC3 content was 57.98%, suggesting that genes favored codons ending with G or C. The effective number of codons (ENC) value range from 38.46 to 61, which indicates that these genes have low codon usage bias. The neutrality plot and ENC-plot analysis revealed that many factors such as mutation and selective pressure play an important role in shaping codon usage bias in P. umbellatus genes. Twenty-two optimal codons were identified as being biased toward codons ending with G or C using the high expression superior codon analysis method. This study will lay a foundation for future research on genetic engineering and molecular evolution in P. umbellatus.

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC₁₂ and GC₃ was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC₃ vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

Synonymous Codon Usage Controls Various Molecular Aspects

Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.

Analysis of codon usage bias based on Fritillaria cirrhosa transcriptome / 中国中药杂志

Understanding of codon usage bias of Fritillaria cirrhosa can provide theoretical basis for heterologous biosynthesis of F. cirrhosa alkaloids by genetic engineering technology. A total of 9 843 full length coding sequences (CDS) from the F. cirrhosa transcriptome data were used for the analysis of codon usage bias. The GC and GC3s contents, effective number of codons(ENC) and relative synonymous codon usage (RSCU) were calculated using the CodonW software. The results show that the codon usage bias value is low in the CDS of F. cirrhosa. A total of 15 codons, including UUG, CUU, AUU, GUU, UCA, CCU, CCA, ACU, ACA, GCA, UAU, CAU, AAU, AGA and GGA, were identified as optimal codons in F. cirrhosa. The optimal codons generally end with A/T at the third codon position. By the transcriptome annotation, we found 26 CDSs possibly involved in the biosynthesis of alkaloids in the F. cirrhosa. The proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae are low in these CDSs. We also proposed a method for the codonoptimization in these target genes. Our work lays the foundation for further study on the biosynthesis of alkaloids of the F. cirrhosa in heterologous species.

Codon Usage Bias and Determining Forces in Taenia solium Genome

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Codon Usage Bias of Human Cytomegalovirus Genes with Different Evolutionary Conservancy

Human cytomegalovirus (HCMV) is a member of beta-herpesvirus and contains a double-stranded genome with longer than 230 Kbp. HCMV infection of human is mostly asymptomatic, but often causes fatal diseases in immunocompromised people. In this study, codon usages of HCMV genes were analyzed and attempted to correlate with evolutionary conservancy. Core genes are the most conserved genes common among herpesvirus family, beta-herpes genes are common to beta-herpesviruses, and CMV genes are the least conserved found only in CMVs. Core genes had higher codon adaptation index (CAI) and GC content of silent 3rd codon position (GC3s) values and lower effective number of codons (Nc) and Nc/GC3s values than CMV genes. The average length of core genes was statistically longer than CMV genes, and core genes were found to be less varied than CMV genes. beta-herpes genes could be placed between core and CMV genes. Higher CAI and GC3s values along with lower Nc and Nc/GC3s values are suggestive of higher codon usage bias and more adaptation to host cells. Thus it is concluded that core genes of HCMV are more biased in codon usage and adapted to host cells compared to CMV genes.

Characterization of Synonymous Codon Usage Bias in the Pseudorabies Virus US1 Gene / 中国病毒学·英文版

In the present study,we examined the codon usage bias between pseudorabies virus (PRV) US1 gene and the US1-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 US1-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 US1-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 of E.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.coli.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.

Three tubulin genes of Trichoderma harzianum: alpha, beta and gamma

Three tubulin genes of Trichoderma harzianum were cloned followed genomic walking procedure. The tubulins showed high degree of amino acid homology with other fungal tubulins and were homologous with each other with 32 to 38 percent amino acid identity. Three measures for the degree of codon usage bias indicated the presence of bias in all the sequences, suggesting high expression levels in all the genes. Protein structures were modeled to provide the basis for understanding the tubulin's properties and its interactions with microtubule-associated proteins. Potential motifs were also postulated.

Translational selection on SHH genes

Codon usage bias has been observed in various organisms. In this study, the correlation between SHH genes expression in some tissues and codon usage features was analyzed by bioinformatics. We found that translational selection may act on compositional features of this set of genes.

Analysis of Synonymous Codon Usage Bias in 09H1N1 / 中国病毒学·英文版

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.