Relative Synonymous Codon Usage Values Research Articles

Study of Codon Usage Patterns and Influencing Factors in Rice Yellow Mottle Virus Based on Coding Sequence Data

Rice yellow mottle virus (RYMV), transmitted by chrysomelids, is one of the major viral pathogens that has devastated rice production in Sub-Saharan Africa. RYMV is a member of the genus Sobemoviruses in the family Solemoviridae and harbors a positive-sense single-stranded RNA (+ssRNA). Here, we used 50 RYMV strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that GC-ended codons were more frequently used in the genome of RYMV. Further low codon usage bias was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested the dominant factor of natural selection was involved in the structuring of CUB in RYMV. Based on RSCU values, the RYMV and its host relationship indicate that the RYMV develops codon usage patterns similar to its host. Generally, both natural selection and mutational pressure impact the codon usage pattern of the protein-coding genes in RYMV. This study is important because it characterized the codon usage pattern in the RYMV genomes and provided the necessary data for a basic evolutionary study on them. Additionally, we recommend that experiments such as whole genome sequencing (WGS) or dual RNA sequencing (DRS) should be considered in order to correlate these in-silico findings with viral diseases in the future.

Evolutionary dynamics of codon usages for peste des petits ruminants virus.

Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.

Codon usage of host-specific P genotypes (VP4) in group A rotavirus

BackgroundGroup A rotavirus (RVA) is a common causative agent of acute gastroenteritis in infants and young children worldwide. RVA P genotypes, determined by VP4 sequences, have been confirmed to infect humans and animals. However, their codon usage patterns that are essential to obtain insights into the viral evolution, host adaptability, and genetic characterization remained unclear, especially across animal hosts.ResultsWe performed a comprehensive codon usage analysis of eight host-specific RVA P genotypes, including human RVA (P[4] and P[8]), porcine RVA (P[13] and P[23]), and zoonotic RVA (P[1], P[6], P[7] and P[19]), based on 233 VP4 complete coding sequences. Nucleotide composition, relative synonymous codon usage (RSCU), and effective number of codons (ENC) were calculated. Principal component analysis (PCA) based on RSCU values was used to explore the codon usage patterns of different RVA P genotypes. In addition, mutation pressure and natural selection were identified by using ENC-plot, parity rule 2 plot, and neutrality plot analyses. All VP4 sequences preferred using A/U nucleotides (A: 0.354-0.377, U: 0.267-0.314) than G/C nucleotides across genotypes. Similarly, majority of commonly used synonymous codons were likely to end with A/U nucleotides (A: 9/18-12/18, U: 6/18-9/18). In PCA, human, porcine, and zoonotic genotypes clustered separately in terms of RSCU values, indicating the host-specific codon usage patterns; however, porcine and zoonotic genotypes were partly overlapped. Human genotypes, P[4] and P[8], had stronger codon usage bias, as indicated by more over-represented codons and lower ENC, compared to porcine and zoonotic genotypes. Moreover, natural selection was determined to be a predominant driver in shaping the codon usage bias across the eight P genotypes. In addition, mutation pressure contributed to the codon usage bias of human genotypes.ConclusionsOur study identified a strong codon usage bias of human RVA P genotypes attributable to both natural selection and mutation pressure, whereas similar codon usage bias between porcine and zoonotic genotypes predominantly attributable to natural selection. It further suggests possible cross-species transmission. Therefore, it warrants further surveillance of RVA P genotypes for early identification of zoonotic infection.

Codon usage divergence of important functional genes in Mycobacterium tuberculosis

Sequence characteristics are usually used to explain the adaptive ability to hosts, metabolism, genetic diversity, drug resistance, and infectivity of Mycobacterium tuberculosis. Exploring the codon usage pattern of coding sequences in Mycobacterium tuberculosis is of great significance. In the present study, two hundred random complete genomes of Mycobacterium tuberculosis were downloaded from the National Center for Biotechnology Information database. The important codon usage pattern, such as the codon bias index, the effective number of codons, the relative synonymous codon usage as well as the base component, of twenty one specific functional genes were counted or calculated. The differences of the relative synonymous codon usage values among those functional genes, and the summation of the standard deviations of codon usage parameters were used to evaluate the divergence degree of the concerned genes. The results show that among the concerned genes, 1) all genes are high GC sequences, the codon usage frequency corresponding to each amino acid of these functional genes had a significant bias; 2) the genes of those with high effective number of codons, such as the coding sequences of Myco-bacterial membrane protein large family, usually have higher divergences; and 3) genes with lower divergences, such as the ag85A and the sigH, are usually highly conserved and are often used as drug target genes. The findings of the present work would improve new understandings on the evolution of Mycobacterium tuberculosis and on the measures to prevent and control tuberculosis from the gene engineering.

Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses.

Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated. The CUB of NS1 was uneven and codons ending with A/U were preferred. The ENC-GC3 and neutrality plots suggested natural selection as the main determinant for CUB. The RCDI, CAI and SiD values showed that the viruses had a high degree of adaptability to human. A total of 2155 human genes showed significant RSCU-based correlation (p < 0.05 and r > 0.5) with NS1 coding sequences and was considered as human genes with CUB similar to NS1 gene of IAV subtypes. Differences and similarities in the subtype-specific human protein–protein interaction (PPI) networks and their functions were recorded among IAVs subtypes, indicating that NS1 of each IAV subtype has a specific pathogenic mechanism. Processes and pathways involved in influenza, transcription, immune response and cell cycle were enriched in human gene sets retrieved based on the CUB of NS1 gene of IAV subtypes. The present work may advance our understanding on the mechanism of NS1 in human infections of IAV subtypes and shed light on the therapeutic options. Supplementary InformationThe online version contains supplementary material available at 10.1007/s10709-022-00155-9.

Variation in the Mitochondrial Genome of the Chagas Disease Vector Triatoma infestans (Hemiptera: Reduviidae).

Chagas' disease is transmitted mainly by members of the subfamily Triatominae (Hemiptera: Reduviidae). Among them, Triatoma infestans (Klug) is the main vector of the disease in Southern Cone of Latin America. In order to contribute to knowledge of the genetic variation between triatomine vectors, in the present study, we analyzed the intraspecific and interspecific variations of the seven mitogenomes available from Triatominae. In addition, in order to examine their evolutionary relationships with others species of Reduviidae and to estimate the divergence time of the main lineages, we constructed phylogenetic trees including mitogenome sequences of 30 species from Reduviidae. Comparative analysis between mitochondrial DNA sequences from two specimens of T. infestans revealed a total of 54 variable sites. Triatoma infestans, Triatoma dimidiata (Latreille), Triatoma rubrofasciata (De Geer), Triatoma migrans (Breddin), Rhodnius pictipes (Stål), and Panstrongylus rufotuberculatus (Champion) present similar mitogenome organization and the length differences observed among these species are primarily caused by variations in control region (CR) and intergenic spacers (IGS). The relative synonymous codon usage values (RSCU) were similar in the six species of Triatominae, and in agreement with the observed in other insects, a biased use of A and C nucleotides in the majority strand was detected. The monophyly of five subfamilies was strongly supported (Phymatinae, Peiratinae, Triatominae, Stenopodainae, and Harpactorinae), while the sampled species of Reduviinae were grouped with one specie from the Salyavatinae subfamily. The oldest subfamily is Phymatinae at 100.3 Mya (99.6-102.2 Mya) and the youngest is Triatominae and Stenopodainae at 52.6 Mya (42.5-63.7 Mya). The estimated diversification time for the Triatominae subfamily agrees with the Andean uplift geological event. An analysis with more mitogenomes from more Triatominae species would be necessary to provide sufficient evidence to support this finding.

Codon usage bias and purifying selection identified in Cirrhinus reba mitogenome

In our previous study, we described sequence assembly and organization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba (GenBank accession no.: MN862482). In this study, our attempts were to find out any mutation or selection pressures and codon usage patterns existing in the mitogenome of the same fish. We applied bioinformatics tools to measure important gene parameters including AT/GC skewness, codon adaptation index (CAI), the effective number of codons (ENc) and GC percentages of each protein coding gene. We found an overrepresentation of A and C resulting a lower number of T and G bases, respectively, where AT-skew was slightly positive and GC-skew was slightly negative. Except for ND6, all protein coding genes (PCGs) had negative GC-skew, which indicated the higher occurrence of Cs. With reference to other two mitogenomes, the dN/dS or Ka/Ks ratios ranged from the lowest value (0.016) for ND4L to the highest value (0.694) for ND1 gene which indicated that PCGs of this fish evolved under strong purifying selection. We further analyzed the codon frequency and relative synonymous codon usage (RSCU) and observed a total of 3802 codons which were used for coding 20 amino acids by a standard set of 64 codons. The amino acids Leucine and Serine were encoded each by six different codons, whereas rest of the amino acids was encoded by either two or four codons. We identified a total of 25 RSCU values (&gt; 1) and revealed 12 codons as “overpresented” that implied for codon usage bias to engage in highly expressed genes for efficient protein synthesis via translational selection. The existence of codon usage biasness rolling in translational selection and the signs of purifying selection identified in PCGs suggest obvious conservation of this threatened fish species.

Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

Sesamum indicum is an ancient oil crop grown in tropical and subtropical areas of the world. We have analyzed 23,538 coding sequences (CDS) of S. indicum to understand the factors shaping codon usage in this important oil crop plant. We identified eleven highly preferred codons in S. indicum that have AT-endings. The slope of a neutrality plot was less than one while effective number of codons (ENC) plot showed distribution above and below the standard curve. There is a significant relationship between protein length and relative synonymous codon usage (RSCU) at the primary axis while there is a weak correlation between protein length and Nc values. Correspondence analysis conducted on RSCU values differentiated CDS based on their GC content and their characteristic feature and showed a discrete distribution. Moreover, by determining codon usage, we found out that majority of the lignan biosynthesis related genes showed a weaker codon usage bias. These results provide insights into understanding codon evolution in sesame.

Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.

The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold

Genome sequencing of Pseudoalteromonas shioyasakiensis D1497, a psychrophile from the Yap trench, revealed that it contained a circle chromosome of 3,631,285 bp with 40.94% GC content and prefered to use codons with A/T in the third position. Additionally, the relative synonymous codon usage (RSCU) values indicated the codons with A and T in the third position were always the most used. Cultivation of P. shioyasakiensis D1497 presented lower substrate consumption rate, higher ATP pool and higher conversion rate of biomass per unit substrate consumed at low temperature (15 °C) than that of the room temperature (25 °C) culture. Comparative transcriptomic analysis revealed that the mRNA abundance of energy metabolism related genes was decreased in 15 °C culture compared with that of 25 °C culture. In addition to its codon usage biases profile, P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold, converting more carbon source into biomass in cold environment.

Compositional features and pattern of codon usage for mitochondrial CO genes among reptiles

The phenomenon of non-random occurrence of synonymous nucleotide triplets (codons) in the coding sequences of genes is the codon usage bias (CUB). In this study, we used bioinformatic tool kit to analyze the compositional pattern and CUB of mitogenes namely COI, COII and COIII across different orders of reptiles. Estimation of overall base composition in the protein-coding sequences of COI, COII and COIII genes of the reptilian orders revealed an uneven usage of nucleotides. The overall count of A nucleotide was found to be the highest while the overall count of G nucleotide was the least. The CO genes across the three reptilian orders were prominently AT biased. Comparison of the GC proportion at each codon position displayed that GC1 percentage ranked the highest in all the three CO genes of the reptilian orders. SCUO values indicated weaker CUB, while considerable variation of SCUO values existed in the three CO genes across the studied reptiles. Relative synonymous codon usage (RSCU) values indicated that mostly the A ending codons were preferred. Based on the parameters namely neutrality plot, mutational responsive index and translational selection, we could conclude that natural selection was the major evolutionary force in COI, COII and COIII genes in the studied reptilian orders. However, correspondence analysis, parity plot and correlation studies indicated the existence of mutation pressure as well on the CO genes.

Comparative analysis of codon usage patterns of FUT2 from different species

Enterotoxigenic E. coli is an important zoonotic pathogen causing diarrhea in human and newborn animals. α - (1,2) fucosyltransferase 2 (FUT2) is closely associated with the formation of pathogenic receptors of Enterotoxigenic E. coli. Codon usage bias analysis can help to better understand the molecular mechanisms and evolutionary relationships of a particular gene. In order to understand the codon usage pattern of FUT2 gene, FUT2 gene coding sequences of nine species were selected from GenBank database for calculating the nucleotide composition (GC content) and genetic indices including effective number of codons, relative synonymous codon usage and relative codon usage bias using R software, in order to analyze codon usage bias and base composition in FUT2 gene from different species. The results showed that the codon usage of FUT2 gene in different species was affected by GC bias, especially GC frequency at the third position of codon (GC3). Most of the optimal codons were biased towards the G/C-ending types. GCC, CUG, UCC, GUG and AUC showed the highest relative synonymous codon usage value among different species, belonging to the most dominant codons. The usage characteristic of the codens for FUT2 gene in Sus scrofa was similar to that of Bos taurus; Homo sapiens was similar to Pan troglodytes. Effective number of codons was significantly, negatively correlated with GC3, and the relative higher frequency of optimal codon implied that FUT2 genes from different species had a strong bias in codon usage.

Codon usage pattern and genetic diversity in chloroplast genomes of Panicum species.

Exploring the molecular identities and the genetic diversity of a plant species is crucial in figuring out the evolutionary pressure of genes as well as in molecular breeding application. Nineteen chloroplast genomes of Panicum species in the National Center for Biotechnology Information database were downloaded and analyzed. The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index and the codon adaptation index of all genes in all chloroplast genomes, as well as the correlation coefficient among them, were calculated and discussed. The correspondence analysis and the clustering characteristics among nineteen genomes base on the relative synonymous codon usage values of nineteen chloroplast genomes were calculated and analyzed. In order to figuring out the evolutionary diversity of certain genes, the codon usage pattern of forty-one typical genes were separately counted and compared. Summations of their standard deviations were considered to evaluate their genetic diversities. The results of codon usage pattern showed that all genes were obvious AU-rich ones in chloroplast genomes of Panicum species, revealing that the natural selection was the main factor that influenced their evolutionary process. The correspondence and clustering analysis among nineteen chloroplast genomes showed that the overall evolutionary differences among them were not significant. However, the analysis on the genetic diversity of tyical genes showed that the degrees of diversity are different, and that the shorter sequences are more prone to instability. These findings would improve our understanding on the evolution of chloroplast genomes of Panicum species and be useful for further study on their evolutionary phenomenon.

Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV.

BackgroundCOVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the relationships between these two types of viruses.ObjectiveTo compare relative synonymous codon usage of ORF1ab gene in SARS-CoV-2 and SARS-CoV, relative synonymous codon usage of their genomes are studied in this paper from the bioinformatics perspective.MethodsThe ORF1ab gene, which is an important non-structural polyprotein coding gene and now used for nucleic acid detection markers in many measurement method, in both SARS-CoV-2 (30 strains) and SARS-CoV (20 strains) are considered to be the research object in the present paper. The relative synonymous codon usage values of the ORF1ab gene are calculated to characterize the differences and the evolutionary characteristics among 50 strains.ResultsThere is a significant difference between SARS-CoV and SARS-CoV-2 when the relative synonymous codon usage value of ORF1ab genes is concerned. The results suggest that codon usage pattern of SARS-CoV is more similar to human than that of the SARS-CoV-2, and that the inner difference in SARS-CoV-2 strains is larger than that of SARS-CoV, which denote the larger diversity exits in the SARS-CoV-2 virus.ConclusionThese results show that the relative synonymous codon usage values in the coronavirus could be used for further research on their evolutionary phenomenon.

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

Plants cannot uptake the insoluble form of phosphate from soil. Phosphate-solubilizing microbes (PSMs) release gluconic acid (C6H12O7) that is synthesized by the interaction between co-factor pyrroloquinoline quinine (PQQ) and glucose dehydrogenase within themselves and hence convert the insoluble phosphate into a soluble form. Phylogenetic analyses based on individual sequences of PqqA–PqqE proteins involved in the PQQ biosynthetic pathway manifested clear clustering formation of the selected species according to their respective genera such asPantoea, Rouxiella, Rahnella, Kosakonia, Mixta, Cronobacter, andSerratia. In multiple sequence alignment (MSA), numerous semi-conserved sites were identified that indicate acquired mutation during evolution. The selectedpqqgenes that appeared within an operon system sustain a specified order viz.pqqABCDEfor both positive and negative strands. The nucleotide composition of the encoding genes displayed higher content of GCs at different positions of the codons and has also been properly reflected in relative synonymous codon usage (RSCU) values of the codons with few exceptions. The correspondence analysis (COA) based on RSCU proclaimed that thepqqBgenes prefer A/U-ending codons over G/C, while for thepqqEgene, G/C-ending codons are comparatively more preferable (except CGU). Mutational pressure contributes to shaping the codon usage pattern for the selectedpqqgenes evinced from the COAs, while the ENc and neutrality plot gives attestation of natural selection. The higher values of CAI indicate the gene adaptability and codon usage bias. These comprehensive computational studies can be beneficial for further research in molecular phylogenetics, genomics, and proteomics and to better understand the evolutionary dynamics of PQQ.

Prediction of gene expression under drought stress in spring wheat using codon usage pattern.

Spring wheat (Triticum aestivum) is a staple food providing sources of essential proteins for human. In fact, gene expressions of wheat play an important role in growth and productivity that are affected by drought stress. The objective of this work focused on analysis gene feature on spring wheat represented by nucleotide and gene expressions under drought stress. It was found that the higher codon adaptation index was in both wheat root and L-galactono-1, 4-lactone dehydrogenase. It was also found that guanine and cytosine content were high (55.56%) in wheat root. Whereas, guanine and cytosine content were low (41.28%) in L-galactono-1, 4-lactone dehydrogenase. Moreover, the higher relative synonymous codon usage value was observed in codon CAA (1.20), GAA (1.33), GAT (1.00), and ATG (1.00) in wheat root and thus about 62.95% of the total variation in relative synonymous codon was explained by principal component analysis. Additionally, high averages frequency number of codon were (above 15.76) in Met, Lys, Ala, Gly, Phe, Asp, Glu, His, and Tyr; whereas, low averages were in remaining amino acids and majority (90%) of modified relative codon bias values was between 0.40 and 0.90. Shortly, calculations and analysis of codon usage pattern under drought stress would help for genetic engineering, molecular evolution, and gene prediction in wheat studies for developing varieties that associate with drought tolerance.

Genomewide comparative analysis of codon usage bias in three sequenced Jatropha curcas

Jatropha curcas has recently emerged as an important bioenergy plant which is an ideal alternative for fossil fuels. It is particularly significant to analyse the codon usage bias (CUB) and further evaluate the intraspecific genetic divergence of three J. curcas in Asia, considering its potential economic benefits and various utilities. In the present study, the patterns of CUB were systematically compared, and the factors shaping CUB were identified in all three genomes of J. curcas. Our observations indicate that the preference for A/T nucleotides and A/T ending codons was present in all the three genomes. Moreover, 11 identical high-frequency codons as well as the optimal expression receptor Nicotiana tabacum were confirmed. Besides, it was observed that CUB resulted from the combined effects of natural selection and mutation pressure, while the natural selection was the determining factor. Eventually, similarity indices based on relative synonymous codon usage (RSCU) values implied low intraspecific genetic divergence in three Asian J. curcas. This study provides useful clues for improving the expression level of exogenous genes and optimizing breeding programmes by molecular-assisted breeding in J. curcas.

Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis

Abstract The evolution of Gnetales is ambiguous, and their phylogenetic position is still debated. The biological and molecular processes may evolve with the evolutionary history of a species or a clade. The molecular/biological processes of phylogenetically similar lineages closely follow their evolutionary pattern. If Gnetales evolved as a sister to Pinaceae, cupressophytes or Coniferales as a whole, then it is expected that the molecular or biological processes may reflect this pattern of evolution. In light of this, we deciphered the codon usage pattern of Gnetales, compared it with angiosperms, Pinaceae, cupressophytes and Coniferales as a whole. We evaluated whether this important molecular process has evolved in agreement with the Anthophyte, Gnepine, Gnecup or Gnetifer hypothesis. We observed that Gnetales prefer A/U-ending codons to G/C-ending codons like other lineages. Natural selection plays a dominant role in governing the codon usage bias (CUB). The CpA/CpT dinucleotides were over-represented, whereas the CpG dinucleotide was suppressed. Hierarchical clustering (HC) and correspondence analysis (CA) on relative synonymous codon usage values of 59 synonymous codons showed Gnetales as a sister clade to Coniferales as a whole and revealed that the codon usage pattern in Gnetales has evolved in close accordance with the Gnetifer hypothesis.

Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae.

The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.Electronic supplementary materialThe online version of this article (10.1007/s00705-020-04890-2) contains supplementary material, which is available to authorized users.

Analysis of Codon Usage Patterns in the Human Papillomavirus Oncogenes

Background: Persistent high-risk genital human papillomavirus (HPV) infection is a major cause of cervical cancer in women. The products of the viral transforming genes E6 and E7 in the high-risk HPVs are known to be similar in their amino acid composition and structure. We performed a comparative analysis of codon usage patterns in the E6 and E7 genes of HPVs. Methods: The E6 and E7 gene sequences of eight HPV subtypes were analyzed to determine their nucleotide composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), neutrality, genetic variability, selection pressure, and codon adaptation index (CAI). Additionally, a correspondence analysis (CoA) was performed. Results: The analysis to determine the effects of differences in composition on the codon usage patterns revealed that there may be usage bias for ‘A’ nucleotides. This was consistent with the results of the RSCU analysis, which demonstrated that the selection of A/T-rich patterns and the preference for A/T-ended codons in HPVs are influenced by compositional constraints. Moreover, the results reveal that selection pressure plays an important role in the CoA results for the RSCU values, Tajima’s D tests, and neutrality tests. Conclusion: The results of this study are consistent with previous findings that most papillomavirus genes are under purifying selection pressure, which limits changes to the encoded proteins. Natural selection and mutation pressures resulting in changes in the nucleotide composition and codon usage bias in the two tumor genes of HPV act differently during the evolution of the HPV subtype; thus, throughout the viral life cycle, HPV can constantly evolve to adapt to a new environment.