Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.

https://link.springer.com/content/pdf/10.1007%2Fs00705-020-04533-6.pdf

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Novel H7N9 influenza virus transmitted from birds to human and, since March 2013, it has caused five epidemic waves in China. Although the evolution of H7N9 viruses has been investigated, the evolutionary changes associated with codon usage are still unclear. Herein, the codon usage pattern of two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), was studied to understand the evolutionary changes in relation to host, epidemic wave, and pathogenicity. Both genes displayed a low codon usage bias, with HA higher than NA. The codon usage was driven by mutation pressure and natural selection, although the main contributing factor was natural selection. Additionally, the codon adaptation index (CAI) and deoptimization (RCDI) illustrated the strong adaptability of H7N9 to Gallus gallus. Similarity index (SiD) analysis showed that Homo sapiens posed a stronger selection pressure than Gallus gallus. Thus, we assume that this may be related to the gradual adaptability of the virus to human. In addition, the host strong selection pressure was validated based on CpG dinucleotide content. In conclusion, this study analyzed the usage of codons of two genes of H7N9 and expanded our understanding of H7N9 host specificity. This aids into the development of control measures against H7N9 influenza virus.

https://www.mdpi.com/1422-0067/21/19/7129/pdf

Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus.

Transfer RNAs (tRNAs) are the most heavily modified RNA species in life entities. Post-transcriptional modifications severely impact the structure and function of tRNAs. To date, hundreds of modifications have been identified in tRNAs, mainly from microorganisms and animals. However, tRNAs in plant roots or tubers that have been widely used for food and medical purpose for centuries are rarely studied because isolation of RNA from plants still remains a challenge. In this paper, a polysaccharase-aided RNA isolation (PARI) method for extraction of high-quality RNA from plants containing large quantities of polysaccharides is developed. This method presents a new strategy of "digesting" polysaccharides that is completely different from the conventional method of "dissolving" the contaminants. By using this method, RNA of high integrity and purity were successfully extracted from ginseng roots because polysaccharide contaminations were removed efficiently with α-amylase digestion. Ginseng tRNAs were first sequenced by NGS and a total of 41 iso acceptors were identified. ChloroplastictRNAGly(GCC) in ginseng root was purified and four modified nucleosides, including m7G, D, T, and Ψ, were identified by LC-MS/MS. The results also revealed that the m7G occurs at a novel position 18, which may be related to the deformation of D-loop. PARI is the first enzyme-assisted technique for RNA isolation from plants, which could fundamentally solve the problem of polysaccharide contaminations. By using the PARI method, more individual tRNAs could be isolated easily from polysaccharide-rich plant tissues, which would have a positive impact on the feasibility of research on structure and function of tRNA in plants.

LC-MS/MS Profiling of Post-Transcriptional Modifications in Ginseng tRNA Purified by a Polysaccharase-Aided Extraction Method

Codon usage divergence of important functional genes in Mycobacterium tuberculosis.

There have been at least four types of dengue outbreaks in the past few years. The evolutionary characteristics of dengue viruses have aroused great concerns. The evolutionary characteristics of dengue 4 viruses are studied in the present study based on their base usage patterns and codon usage patterns. The effective number of codons and relative synonymous codon usage (RSCU) values of four types of dengue viruses were counted or calculated. The Kullback–Leibler (K–L) divergences of relative synonymous codon usage from dengue viruses to humans and the Kullback–Leibler divergences of amino acid usage patterns from dengue viruses to humans were calculated to explore the adaptation levels of dengue viruses. The results suggested that: (1) codon adaptation in dengue 4 viruses occurred through an evolutionary process from 1956 to 2021, (2) overall relative synonymous codon usage values of dengue 4 viruses showed more similarities to humans than those of other subtypes of dengue viruses, and (3) the smaller Kullback–Leibler divergence of amino acid usage and relative synonymous codon usage from dengue viruses to humans indicated that the dengue 4 viruses adapted to human hosts better. All results indicated that both mutation pressure and natural selection pressure contributed to the codon usage pattern of dengue 4 viruses more obvious than to other subtypes of dengue viruses and that the dengue 4 viruses adapted to human hosts better than other types of dengue viruses during their evolutionary process. 

https://www.frontiersin.org/articles/10.3389/fmicb.2022.935678/pdf

Componential usage patterns in dengue 4 viruses reveal their better evolutionary adaptation to humans

Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species.

Panax ginseng is usually used as a famous plant medicine in many countries. In order to study the codon usage in whole chloroplast genome in Panax ginseng, whole chloroplast genome sequence is analyzed via codonW software and some results such as relationships between the codon adaptation index, frequency of optimal codons, codon bias index, effective number of codons, especially the relative synonymous codon usage are all discussed. Furthermore, PR2-bias plot, histogram GC content, Codon Bias Index are also analyzed for exploring the sequence characteristics of chloroplast genome in Panax ginseng. These results showed that codon usage bias in the chloroplast genome from Panax ginseng is weak, and the relative results could lay a foundation for other further study on the medicinal plant Panax ginseng.

/pdf/codon-usage-study-on-chloroplast-genome-in-medicinal-plant-49trabw3ka.pdf

Codon Usage Study on Chloroplast Genome in Medicinal Plant Panax Ginseng

ADPKD is associated with large interfamilial and intrafamilial variability [1]. Many scientists studied the mechanism [2-5] of the ADPKD and its treatment from various methods [6-8]. Form the genome perspective, there are two mutations have been found to be associated with adpkdPKD1 and PKD2 [9-12]. They are respectively on the 16th and 4th chromosomes [13-15]. Most of the ADPKD are caused by PKD1 mutation. Most of the patients with ADPKD may require dialysis or kidney transplantation eventually [16-18]. Therefore, it is necessary to study the ADPKD from the perspective of genome. Many scientists such as Tao Yang, et al, explored the novel mutations of PKD1 gene in Chinese patients with ADPKD by targeted nextgeneration sequencing [19], Consugar, et al. studied the characteristics of large rearrangements in ADPKD and the PKD1/TSC2 contiguous gene syndrome [20]. Furthermore, Pathogenicity [21], inactivation [22], development [23] of the PKD1 were also studied by many scientists. In this paper, based on the previous studies, the codon usage characteristics of PKD1 and PKD2 gene is cauculated via the CodonW, and analyzed via the PR2-bias plot analysis: A3 / (A3 + T3) vs. G3 / (G3 + C3) . Then the RSCU values of PKD1 and PKD2 are plotted and discussed.

/pdf/codon-usage-of-autosomal-dominant-polycystic-kidney-disease-35c8nihseg.pdf

Codon Usage of Autosomal Dominant Polycystic Kidney Disease Genes PKD1 and PKD2

ARC Journal of Urology Page |9 Abstract: Urinary prokallikrein in human participates in the regulation of water and electrolyte balance. In this paper, several characteristics of urinary prokallikrein are studied via some bioinformatics tools. First, the chemical and physical properties such as the molecular weight, the isoelectric point and the hydrophobicity, etc, of urinary prokallikrein are predicted via ProtParam tool. The results show that the molecular formula is C1168H1764N310O363S14, the instability index is 37.98, the theoretical pI is 4.57, et al. the secondary structure of urinary prokallikrein is predicted via the SOPMA tool, the result shows that there are 57(23.95%) Alpha helix, 60(25.21%) Beta sheet, 31(13.03%) Turn and 90(37.82%) Coil. Finally, phosphorylation sites and the protein-protein interaction of urinary prokallikrein are respectively studied by the netphos tool and the STRING system.

/pdf/bioinformatics-tools-stuty-on-the-sequence-and-structure-3ztxfo3dxf.pdf

Bioinformatics Tools Stuty on the Sequence and Structure Characteristics of Urinary Prokallikrein

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Papers

Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species.

Codon Usage Study on Chloroplast Genome in Medicinal Plant Panax Ginseng

Codon Usage of Autosomal Dominant Polycystic Kidney Disease Genes PKD1 and PKD2

Bioinformatics Tools Stuty on the Sequence and Structure Characteristics of Urinary Prokallikrein