Intrastrand parity rules of DNA base composition and usage biases of synonymous codons

Ross River virus genomes from Australia and the Pacific display coincidental and antagonistic codon usage patterns with common vertebrate hosts and a principal vector

Around 4500 Ross River virus (RRV) human cases are reported in Australia annually. To date, there is no registered nor licenced vaccine to protect against RRV disease. Identifying and substituting preferred with less-preferred codons and dinucleotides is a recognised strategy to attenuate viruses and may prove useful to vaccine development efforts for RRV and other related viruses. Here, we used bioinformatic approaches aimed at assessing evidence of codon usage and dinucleotide bias in 55 RRV whole genomes sampled from humans (Homo sapiens), macropods (Notomacropus agilis), and the Aedes vigilax mosquito. Our results indicate that RRV undergoes positive and negative codon usage bias with natural selection as the major force driving RRV codon usage patterns. RRV displays a bias towards codons with an A or C at the 3rd position while H. sapiens displays a G or C and N. agilis and Ae. vigilax both show bias towards codons with an A or U at the same 3rd position. RRVs codon usage patterns are coincidental to those displayed by common vertebrate hosts and antagonistic to patterns of Ae. vigilax. The coincidental bias identified suggests vertebrate host gene expression greatly influences RRV evolution. In addition, we show that the UG dinucleotides in RRV are overrepresented at all three codon sites, while CA dinucleotides are only overrepresented at codon sites 1-2 and 2-3. These over and under-representations can be exploited to develop attenuated RRV RNA vaccines. The approach utilised here could also be used to develop vaccines for other alphaviruses of global importance.

Genetic characterization of four bacteriophages of Salmonella enterica derived from different geographic regions in China via genomic comparison

Based on the AT content > GC content in four Salmonella enterica lytic bacteriophage genomes, information entropy analysis revealed that overall nucleotide usage bias is shaped in the gene population. This genetic feature directly contributes to synonymous codons tending toward the A/T end rather than the C/G end. Furthermore, the interplay between the nucleotide composition constraint from the bacteriophage itself and the natural selection caused by outside environments forces our bacteriophages into similar evolutionary trends in terms of overall codon usage patterns. We identified the nucleotide composition constraint which plays an important role in shaping synonymous codon usage patterns including the keto skew at the first codon position, the pyrimidine skew at the second position and the AT skew at the third position. Although the four bacteriophages were isolated from different geographical regions in China, they display similar evolutionary trends in terms of genomic organization and synonymous codon usage, which are strongly influenced by the nucleotide composition constraint of the bacteriophage. The findings of the present study reveal important details of the evolutionary and host-pathogen interactions of Salmonella enterica, which will benefit the efficient utilization of phages for therapeutic and other applications.

Decoding codon usage in human papillomavirus type 59

Human Papillomavirus Type 59 (HPV-59) is a high-risk subtype linked to cervical and other cancers. However, its codon usage patterns remain underexplored despite their importance in understanding viral behavior and vaccine optimization. This study reveals a mild codon usage bias in HPV-59, with a notable preference for A/T-ending codons and 29 favored codons, primarily ending in A or T. Additionally, CpG dinucleotides were significantly underrepresented, potentially aiding immune evasion. Analyses using the Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicate that both mutational pressure and natural selection shape codon usage, with natural selection playing a dominant role. The virus's codon usage moderately aligns with human translational machinery, as shown by the Isoacceptor tRNA pool, Codon Adaptation Index, and Relative Codon Deoptimization Index, reflecting an evolutionary balance between protein synthesis efficiency and host compatibility. These findings provide valuable insights into HPV-59 biology, offering guidance for developing optimized vaccines.

Analysis of Codon Usage Patterns in a Rare Palmitoleic Acid Production Oleaginous Yeast, Scheffersomyces segobiensis

Scheffersomyces segobiensis DSM27193 has been identified as a potential host for Palmitoleic acid (POA)-rich lipids production. Our previous study has found that S. segobiensis DSM27193 possesses a broad substrate spectrum, excellent xylose fermentation capability, rapid growth, high biomass, and an abundance of intracellular acetyl-CoA. These characteristics make S. segobiensis DSM27193 an ideal chassis for metabolic engineering and the synthesis of various chemicals. However, the genetic coding features of this strain remain unclear. Analysis of the internal transcribed spacer (ITS) region suggested that S. segobiensis DSM27193 is closely related to Pichia stipitis (renamed Scheffersomyces stipitis), both of which exhibit CTG coding characteristic. In this study, we utilized software tools, such as CodonW, CUPS, and others to analyze the codon preference of the S. segobiensis DSM27193 genome. Additionally, we validated the reliability of the codon table through the expression of green fluorescent protein (GFP). The analysis results serve as a theoretical foundation for enhancing the expression of exogenous genes in S. segobiensis DSM27193.

Codon Usage Bias: A Potential Factor Affecting VGLUT Developmental Expression and Protein Evolution

More and more attention has been paid to the role of synonymous substitution in evolution, in which codon usage preference can affect gene expression distribution and protein structure and function. Vesicular glutamate transporter (VGLUT) consists of three isoforms, among which VGLUT3 is significantly different from other VGLUTs in functional importance, expression level, and distribution range, whose reason is still unclear. This study sought to analyze the role of codon preference in VGLUT differentiation. To conduct an evolutionary analysis of the three VGLUTs, this paper uses bioinformatics research methods to analyze the coding sequences of the three VGLUTs in different species and compare the codon usage patterns. Furthermore, the differences among the three VGLUTs were analyzed by combining functional importance, expression level, distribution range, gene structure, protein relationship network, expression at specific developmental stages, and phylogenetic tree, and the influence of codon usage pattern was explored. The results showed that the VGLUT with greater codon preference had less functional importance, lower expression levels, more peripheral distribution away from the CNS, smaller exon density of gene, less conserved and farther away from the CDS region miRNA regulatory sites, simpler and less tight protein interaction networks, delayed developmental expression, and more distant evolutionary relationships. Codon usage preference is a potential factor affecting VGLUT developmental expression and protein evolution.

Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus

Synonymous codon usage plays an important role in the adaptation of viruses to their hosts. Bovine viral diarrhea virus (BVDV) relies on a high mutation rate in its genome to achieve the necessary fitness in a particular host. However, the question of which selective forces influence nucleotide pair and synonymous codon usage patterns in different BVDV genotypes remains unresolved. Here, 169 BVDV strains isolated at different times in various countries were analyzed to compare their dinucleotide frequency and synonymous codon usage. Examination of the nucleotide usage pattern in the open reading frame (ORF) of BVDV revealed a significantly higher frequency of purine than pyrimidine, with the highest extent of nucleotide usage bias observed in the first codon position. Moreover, a nucleotide pair bias, especially favoring CpG dinucleotides, was observed in all of the genotypes. Together, the nucleotide composition constraints and nucleotide pair bias appear to have influenced the overall codon usage pattern. Nucleotide pair and synonymous codon usage biases were associated with individual genotypes to different degrees. Of particular note, BVDV-1 exhibited more variation in its nucleotide pair and synonymous codon usage than BVDV-2 and BVDV-3, suggesting that these patterns are shaped both by selection of mutations in the viral genome and translational selection in the host.

Analysis of the Codon Usage Bias Pattern in the Chloroplast Genomes of Chloranthus Species (Chloranthaceae)

BACKGROUND

The codon preference of chloroplast genomes not only reflects mutation patterns during the evolutionary processes of species but also significantly affects the efficiency of gene expression. This characteristic holds significant scientific importance in the application of chloroplast genetic engineering and the genetic improvement of species. Chloranthus, an ancestral angiosperm with significant economic, medicinal, and ornamental value, belongs to the basal angiosperms. However, the codon usage patterns among Chloranthus species have remained unclear.

METHODS

To investigate codon usage bias and its influencing factors in Chloranthus chloroplast genomes, we utilized CodonW, CUSP, and SPSS software to analyze the chloroplast genomes of seven Chloranthus species.

RESULTS

In this study, we reported and characterized the complete chloroplast genome of the Chinese endemic species Chloranthus angustifolius. The phylogenetic tree based on the whole chloroplast genomes showed that C. angustifolius is sister to Chloranthus fortunei, and the genus Chloranthus is divided into two major clades, consistent with previous studies. Our results revealed that the GC content at different codon positions across all seven Chloranthus species was less than 50%, with GC1 > GC2 > GC3. Additionally, the average effective number of codons (ENC) values exceeded 45. A total of 10 shared optimal codons were identified, nine of which end with A or U. PR2-plot, ENC-plot, and neutrality plot analyses indicated that natural selection primarily influenced codon usage bias in the chloroplast genomes of Chloranthus.

CONCLUSIONS

We newly obtained the chloroplast genome of C. angustifolius and proposed that natural selection played a key role in codon usage patterns in Chloranthus species. These findings contribute to our understanding of evolutionary history and genetic diversity within this genus.

Codon usage analysis in selected virulence genes of Staphylococcal species

The Staphylococcus genus, composed of Gram-positive bacteria, includes several pathogenic species such as Staphylococcus aureus, S. epidermidis, S. haemolyticus, and S. saprophyticus, each implicated in a range of infections. This study investigates the codon usage patterns in key virulence genes, including Autolysin (alt), Elastin Binding protein (EbpS), Lipase, Thermonuclease, Intercellular Adhesion Protein (IcaR), and V8 Protease, across four Staphylococcus species. Using metrics such as the Effective Number of Codons (ENc), Relative Synonymous Codon Usage (RSCU), Codon Adaptation Index (CAI), alongside neutrality and parity plots, we explored the codon preferences and nucleotide composition biases. Our findings revealed a pronounced AT-rich codon preference, with AT-rich genomes likely aiding in energy-efficient translation and bacterial survival in host environments. These insights provide a deeper understanding of the evolutionary adaptations and translational efficiency mechanisms that contribute to the pathogenicity of Staphylococcus species. This knowledge could pave the way for novel therapeutic interventions targeting codon usage to disrupt virulence gene expression.

Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias

Members of the families Thermosynechococcaceae and Thermostichaceae are well-known unicellular thermophilic cyanobacteria and a non-thermophilic genus Pseudocalidococcus was newly classified into the former. Analysis of the codon usage bias (CUB) of cyanobacterial species inhabiting different thermal and non-thermal niches will benefit the understanding of their genetic and evolutionary characteristics. Herein, the CUB and codon context patterns of protein-coding genes were systematically analyzed and compared between members of the two families. Overall, the nucleotide composition and CUB indices were found to differ between thermophiles and non-thermophiles. The thermophiles showed a higher G/C content in the codon base composition and tended to end with G/C compared to the non-thermophiles. Correlation analysis indicated significant associations between codon base composition and CUB indices. The results of the effective number of codons, parity-rule 2, neutral and correspondence analyses indicated that mutational pressure and natural selection primarily account for CUB in these cyanobacterial species, but the primary driving forces exhibit variation among genera. Moreover, the optimal codons identified based on relative synonymous codon usage values were found to differ among genera and even within genera. In addition, codon context pattern analysis revealed the specificity of the sequence context of start and stop codons among genera. Intriguingly, the clustering of codon context patterns appeared to be more related to thermotolerance than to phylogenomic relationships. In conclusion, this study facilitates the understanding of the characteristics and sources of variation of CUB and the evolution of the surveyed cyanobacterial clades with different thermotolerance and provides insights into their adaptation to different environments.

Characterization of Complete Mitochondrial Genome and Phylogeny of Three Echeneidae Species

Species of the family Echeneidae are renowned for their capacity to adhere to various hosts using a sucking disc. This study aimed to examine the mitochondrial genome characteristics of three fish species (Echeneis naucrates, Remora albescens, and Remora remora) within the family Echeneidae and determine their phylogenetic relationships. The findings revealed that the mitochondrial genome lengths of the three species were 16,611 bp, 16,648 bp, and 16,623 bp, respectively, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a D-loop region. Most PCGs utilized ATG as the initiation codon, while only cox I used the GTG as the initiation codon. Additionally, seven genes employed incomplete termination codons (T and TA). The majority of PCGs in the three species displayed negative AT-skew and GC-skew values, with the GC-skew amplitude being greater than the AT-skew. The Ka/Ks ratios of the 13 PCGs did not exceed 1, demonstrating these species had been subjected to purification selection. Furthermore, only tRNA-Ser (GCT) lacked the D arm, while other tRNAs exhibited a typical cloverleaf secondary structure. Bayesian inference (BI) and maximum likelihood (ML) methods were utilized to construct a phylogenetic tree of the three species based on the 13 PCGs. Remora remora was identified as a distinct group, while R. osteochir and R. brachyptera were classified as sister taxa. This study contributes to the mitochondrial genome database of the family Echeneidae and provides a solid foundation for further systematic classification research in this fish group.

Genomic compliance with Chargaff's second parity rule may have originated non-adaptively, but stem-loops now function adaptively

Of Chargaff's four rules on DNA base quantity, his second parity rule (PR-2) is the most contentious. Various biometricians (e.g., Sueoka, Lobry) regarded PR-2 compliance as a non-adaptive feature of modern genomes that could be modeled through interrelations among mutation rates. However, PR-2 compliance with stem-loop potential was considered adaptively relevant by biochemists familiar with analyses of nucleic acid structure (e.g., of Crick) and of meiotic recombination (e.g., of Kleckner). Meanwhile, other biometricians had shown that PR-2 complementarity extended beyond individual bases (1-mers) to oligonucleotides (k-mers), possibly reflecting "advantageous DNA structure" (Nussinov). An "introns early" hypothesis (Reanney, Forsdyke) had suggested a primordial nucleic acid world with recombination-mediated error-correction requiring genome-wide stem-loop potential to have evolved prior to localized intrusions of protein-encoding potential (exons). Thus, a primordial genome was equivalent to one long intron. Indeed, when assessed as the base order-dependent component (correcting for local influences of GC%), modern genes, especially when evolving rapidly under positive Darwinian selection, display high intronic stem-loop potential. This suggests forced migration from neighboring exons by competing protein-encoding potential. PR-2 compliance may have first arisen non-adaptively. Primary prototypic structures were later strengthened by their adaptive contribution to recombination. Thus, contentious views may actually be in harmony.

Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51

Human papillomavirus type 51 (HPV-51) is associated with various cancers, including cervical cancer. Examining the codon usage bias of the organism can offer valuable insights into its evolutionary patterns and its relationship with the host. This study comprehensively analyzed codon usage bias in HPV-51 by examining 64 complete genome sequences sourced from the NCBI GenBank database. Our analysis revealed no noteworthy preference for codon usage in HPV-51 overall. However, there was a noticeable bias towards A/T-ending codons, accompanied by GC3s below 32%. Dinucleotide frequency analysis revealed reduced frequencies for ApA, CpG, and TpC dinucleotides, while CpA and TpG dinucleotides were more frequent than others. Relative Synonymous Codon Usage analysis revealed 30 favored codons, primarily concluding with A/T nucleotides. Further analysis using Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicated a balance between mutational pressure and natural selection, with natural selection being the primary force shaping codon usage bias. The Isoacceptor tRNA Pool analysis indicates that HPV-51 has a higher translation efficiency within the human cellular translational system. Moreover, the Codon Adaptation Index and Relative Codon Deoptimization Index analyses suggested a moderate adaptation of HPV-51 to human codon preferences. Our discoveries offer valuable perspectives on how HPV-51 evolves and uses genetic codes, contributing to a deeper comprehension of its endurance and disease-causing potential.

Transcriptomic analysis of codon usage patterns and gene expression characteristics in leafy spurge

Leafy spurge (Euphorbia esula) is an important herb and potential energy source with medicinal value. Codon usage bias (CUB) is a static feature of genes and genomes that results from adaptation and selection during long-term evolution and facilitates molecular breeding in transgenic plants. Here, we used TransDecoder to identify candidate coding regions from the downloaded leafy spurge transcriptome and generate coding region annotation files based on reference genomes. The whole genome showed A/T bias, especially at terminal positions, and seven high-frequency codons were identified. We compared codon usage frequencies to identify candidate exogenous expression receptor systems for leafy spurge. The identified factors affecting leafy spurge CUB included natural selection and other factors, mutation pressure and base composition, with natural selection and other factors being dominant. The observed CUB was significantly positively correlated with the gene expression levels. Systematic analysis of whole-genome leafy spurge revealed that highly expressed protein-coding genes presented greater CUB than did less expressed protein-coding genes. Furthermore, the highly expressed genes tended to have terminal G/C bases. In summary, we conducted a series of related studies based on the leafy spurge whole-genome sequence and laid a foundation for selecting suitable exogenous expression receptor systems and improving gene expression levels.

Selection on synonymous codon usage in soybean (Glycine max) WRKY genes

The WRKY transcription factor gene family in soybean [Glycine max (L.) Merr.] (GmWRKY) is critical for the plant's development and stress responses. This study examines the evolutionary dynamics of the GmWRKY gene family, focusing on its synonymous codon usage bias (CUB) in a comprehensive set of 179 coding sequences. CUB was analyzed using various indices, revealing a preference for A/T-ending codons and relatively low codon bias. Codon adaptation index (CAI) analysis suggested that these genes are optimized for efficient translation despite relatively low bias, reflecting a balance between codon diversity and translation efficiency. Neutrality and NC plots indicated that selective forces dominate over mutational forces in shaping codon usage, while selection signature analysis showed purifying selection being prevalent across the gene family. However, episodic positive selection was also detected in certain clades, highlighting potential adaptive diversification in response to environmental stress. Additionally, promoter binding site analysis uncovered correlations between codon usage and transcriptional regulation, indicating a context-dependent relationship between CUB and gene expression. Phylogenetic analysis identified 11 well-supported clades in the modern GmWRKY gene family and ancestral sequence reconstruction revealed more relaxed codon preferences and reduced selection constraints in modern GmWRKY genes, potentially linked to neofunctionalization and adaptation to environmental changes. These findings provide a framework for optimizing gene expression in transgenic soybean crops with resilience. Further functional validation of positively selected genes is recommended to elucidate their role in stress responses.

Characterization, Codon Usage Pattern and Phylogenetic Implications of the Waterlily Aphid Rhopalosiphum nymphaeae (Hemiptera: Aphididae) Mitochondrial Genome

The water lily aphid, Rhopalosiphum nymphaeae, is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of R. nymphaeae was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of R. nymphaeae is 15,772 bp in length, with a high A+T content (84.34%). It contains 37 coding genes (13 protein-coding genes, 22 transport RNAs, and two ribosomal RNAs) and two non-coding regions (one control region and one repeat region). Enc-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of the protein-coding genes is mainly affected by natural selection. The evolution rate analysis (the ratio of nonsynonymous to synonymous, Ka/Ks) indicated that all the PCGs in R. nymphaeae are under a strong purifying selection. The control region has conserved structure elements, and two types of tandem repeat units exist. The length and sequence of the aphid-unique repeat region has high similarity with closely related species. Phylogenetic analyses determined by both maximum likelihood and Bayesian inference support the monophyly of Aphidinae, Aphidini, Aphidina, and Rhopalosiphina. However, the monophyly of the genera in Rhopalosiphina, such as Rhopalosiphum, is still not resolved. This study may help us to understand the phylogenetic relationship of aphids, and much more aphid data are needed in future studies.

Codon Bias of the DDR1 Gene and Transcription Factor EHF in Multiple Species

Milk production is an essential economic trait in cattle, and understanding the genetic regulation of this trait can enhance breeding strategies. The discoidin domain receptor 1 (DDR1) gene has been identified as a key candidate gene that influences milk production, and ETS homologous factor (EHF) is recognized as a critical transcription factor that regulates DDR1 expression. Codon usage bias, which affects gene expression and protein function, has not been fully explored in cattle. This study aims to examine the codon usage bias of DDR1 and EHF transcription factors to understand their roles in dairy production traits. Data from 24 species revealed that both DDR1 and EHF predominantly used G/C-ending codons, with the GC3 content averaging 75.49% for DDR1 and 61.72% for EHF. Synonymous codon usage analysis identified high-frequency codons for both DDR1 and EHF, with 17 codons common to both genes. Correlation analysis indicated a negative relationship between the effective number of codons and codon adaptation index for both DDR1 and EHF. Phylogenetic and clustering analyses revealed similar codon usage patterns among closely related species. These findings suggest that EHF plays a crucial role in regulating DDR1 expression, offering new insights into genetically regulating milk production in cattle.

Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease

Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in understanding the molecular organization of genome. Bioinformatic approach was used to analyze the protein-coding sequences of genes associated with Parkinson's disease (PD) to explore compositional features and codon usage pattern as no details work was reported yet. The average improved effective number of codons (Nc) and Nc prime were 42.74 and 44.26 respectively, indicated that CUB was low in these genes. In most of the genes, the overall GC content was almost 50% and GC content at the 1st codon position was the highest while GC content at the 2nd codon position was lowest. Relative synonymous codon usage (RSCU) analysis elucidated over-represented (p > 1.6) and under-represented codons (p < 0.6). The GTG (Val) is the only codon over-represented in all genes. Over-represented codons except (GTG) were A or T ending while under-represented codons (except ACT) were G or C ending. The codons namely TTA (Leu), CTA (Leu), ATC (Ile), ATA (Ile), AGT (Ser), AAC (Asn), TGT (Cys), TGC (Cys), CGC (Arg), AGA (Arg), and AGG (Arg) were absent in SNCA1 to SNCA8 genes. The codon TCG (Ser) was absent in all genes except UCHL1 and PINK1. Correspondence analysis (COA) revealed that the pattern of codon usage differs among genes associated with PD. Neutrality plot analysis indicated some of the points are diagonal distribution suggested that mutation pressure influenced the CUB in genes associated with PD.

Determination of codon pattern and evolutionary forces acting on genes linked to inflammatory bowel disease

Inflammatory bowel disease (IBD) is an inflammatory disorder of the gastrointestinal tract. The present study attempted to understand the codon usage preferences in genes associated with IBD progression. Compositional analysis, codon usage bias (CUB), Relative synonymous codon usage (RSCU), RNA structure, and expression analysis were performed to obtain a comprehensive picture of codon usage in IBD genes. Compositional analysis of 62 IBD-associated genes revealed that G and T are the most and least abundant nucleotides, respectively. ApG, CpA, and TpG dinucleotides were overrepresented or randomly used, while ApC, CpG, GpT, and TpA dinucleotides were either underrepresented or randomly used in genes related to IBD. The codons influencing the codon usage the most in IBD genes were CGC and AGG. A comparison of codon usage between IBD, and pancreatitis (non-IBD inflammatory disease) indicated that only codon CTG codon usage was significantly different between IBD and pancreatitis. At the same time, there were codons ATA, ACA, CGT, CAA, GTA, CCT, ATT, GCT, CGG, TTG, and CAG for whom codon usage was significantly different for IBD and housekeeping gene sets. The results suggest similar codon usage in at least two inflammatory disorders, IBD and pancreatitis. The analysis helps understand the codon biology, factors affecting gene expression of IBD-associated genes, and the evolution of these genes. The study helps reveal the molecular patterns associated with IBD.

Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes

Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.

Mitochondrial genomes of Macropsini (Hemiptera: Cicadellidae: Eurymelinae): Structural features, codon usage patterns, and phylogenetic implications

Macropsini is a tribe of Eurymelinae in the family Cicadellidae that is widely distributed worldwide. Still, its taxonomic status has been unstable, and the classification of certain clades at the genus level has been controversial. The aim of this study is to address the patterns and processes that explain the structure and the evolution of the mitogenomes of Macropsini, while contributing to the resolution of systematic issues involving five of their genera. To this task, the mitogenomes of 26 species of the tribe were sequenced and characterized, and their phylogenetic relationships were reconstructed. The results revealed that the nucleotide composition of mitochondrial genes in these 26 species was significantly skewed toward A and T. Codons ending with T or A in relative synonymous codon usage were significantly more prevalent than those ending with C or G. The parity plot, neutrality plot, and correspondence analysis revealed that mutation and selective pressure affect codon usage patterns. In the phylogenetic relationships of the Macropsini, the monophyly of Pedionis and Macropsis was well-supported. Meanwhile, Oncopsis revealed paraphyletic regarding Pediopsoides. In conclusion, this research not only contributes the valuable data to the understanding of the mitogenome of the Macropsini but also provides a reference for future investigations on codon usage patterns, potential adaptive evolution, and the phylogeny of the mitogenome within the subfamily Eurymelinae.

RNA editing sites and triplet usage in exomes of bat RNA virus genomes of the family Paramyxoviridae

Bats contain a diverse spectrum of viral species in their bodies. The RNA virus family Paramyxoviridae tends to infect several vertebrate species, which are accountable for a variety of devastating infections in both humans and animals. Viruses of this kind include measles, mumps, and Hendra. Some synonymous codons are favoured over others in mRNAs during gene-to-protein synthesis process. Such phenomenon is termed as codon usage bias (CUB). Our research emphasized many aspects that shape the CUB of genes in the Paramyxoviridae family found in bats. Here, the nitrogenous base A occurred the most. AT was found to be abundant in the coding sequences of the Paramyxoviridae family. RSCU data revealed that A or T ending codons occurred more frequently than predicted. Furthermore, 3 overrepresented codons (CAT, AGA, and GCA) and 7 underrepresented codons (CCG, TCG, CGC, CGG, CGT, GCG and ACG) were detected in the viral genomes. Correspondence analysis, neutrality plot, and parity plots highlight the combined impact of mutational pressure and natural selection on CUB. The neutrality plot of GC12 against GC3 yielded a regression coefficient value of 0.366, indicating that natural selection had a significant (63.4 %) impact. Moreover, RNA editing analysis was done, which revealed the highest frequency of C to T mutations. The results of our research revealed the pattern of codon usage and RNA editing sites in Paramyxoviridae genomes.

The first mitogenome of the genus Amphalius (Siphonaptera: Ceratophyllidae) and its phylogenetic implications

Amphalius spirataenius belongs to Arthropoda, Insecta, Siphonaptera, Ceratophylloidea, Ceratophyllinae, Amphalius. Only 2 species from the subfamily Ceratophyllinae have been sequenced for mitogenomes to date. The genus Amphalius mitogenome research was still blank. The A. spirataenius mitogenome was determined, annotated and analysed for the first time in this study. The 14 825 bp long genome has the typical metazoan of 37 genes with insect ancestral genome arrangement pattern. There was no significant difference in codon usage of 13 protein-coding genes: UUA, UCU, GUU, ACU and GCU were the most frequently used codons. It was found that the reason for codon preference mainly contributed to natural selection base on PR2, ENC-plot and neutrality curve analysis. Evolutionary rate, conserved sites, variable sites and nucleotide diversity analysis indicated that nad6 of A. spirataenius had the fastest evolutionary rate, while cox1 had the slowest evolutionary rate. Phylogenetic trees were reconstructed based on 13 protein-coding genes and 2 rRNA genes datasets using Bayesian inference and maximum likelihood method. The phylogenetic tree supported that both Siphonaptera and Mecoptera were monophyletic, and were sister groups to each other. This study filled gap of the genus Amphalius mitogenome sequences and was of great significance for understanding evolution of the order Siphonaptera.

Comparative Analysis of Codon Usage Bias in Six Eimeria Genomes

The codon usage bias (CUB) of genes encoded by different species' genomes varies greatly. The analysis of codon usage patterns enriches our comprehension of genetic and evolutionary characteristics across diverse species. In this study, we performed a genome-wide analysis of CUB and its influencing factors in six sequenced Eimeria species that cause coccidiosis in poultry: Eimeria acervulina, Eimeria necatrix, Eimeria brunetti, Eimeria tenella, Eimeria praecox, and Eimeria maxima. The GC content of protein-coding genes varies between 52.67% and 58.24% among the six Eimeria species. The distribution trend of GC content at different codon positions follows GC1 > GC3 > GC2. Most high-frequency codons tend to end with C/G, except in E. maxima. Additionally, there is a positive correlation between GC3 content and GC3s/C3s, but a significantly negative correlation with A3s. Analysis of the ENC-Plot, neutrality plot, and PR2-bias plot suggests that selection pressure has a stronger influence than mutational pressure on CUB in the six Eimeria genomes. Finally, we identified from 11 to 15 optimal codons, with GCA, CAG, and AGC being the most commonly used optimal codons across these species. This study offers a thorough exploration of the relationships between CUB and selection pressures within the protein-coding genes of Eimeria species. Genetic evolution in these species appears to be influenced by mutations and selection pressures. Additionally, the findings shed light on unique characteristics and evolutionary traits specific to the six Eimeria species.

The evolutionary and genetic patterns of African swine fever virus

African swine fever (ASF) is a serious animal disease, and has spread to Africa, Europe and Asia, causing massive economic losses. African swine fever virus (ASFV) is transmitted from a reservoir host (warthog) to domestic pigs via a sylvatic cycle (transmission between warthogs and soft ticks) and a domestic cycle (transmission between domestic pigs) and survives by expressing a variety of genes related to virus-host interactions. We evaluated differences in codon usage patterns among ASFV genotypes and clades and explored the common and specific evolutionary and genetic characteristics of ASFV sequences. We analysed the evolutionary relationships, nucleotide compositions, codon usage patterns, selection pressures (mutational pressure and natural selection) and viral adaptation to host codon usage based on the coding sequences (CDS) of key functional genes of ASFV. AT bias was detected in the six genes analysed, irrespective of clade. The AT bias of genes (A224L, A179L, EP153R) encoding proteins involved in interaction with host cells after infection was high; among them, the AT bias of EP153R was the greatest at 78.3%. A large number of overrepresented codons were identified in EP153R, whereas there were no overrepresented codons with a relative synonymous codon usage (RSCU) value of ≥3 in B646L. In most genes, the pattern of selection pressure was similar for each clade, but in EP153R, diverse patterns of selection pressure were captured within the same clade and genotype. As a result of evaluating host adaptation based on the codon adaptation index (CAI), for B646L, E183L, CP204L and A179L, the codon usage patterns in all sequences were more similar to tick than domestic pig or wild boar. However, EP153R showed the lowest average CAI value of 0.52 when selecting tick as a reference set. The genes analysed in this study showed different magnitudes of selection pressure at the clade and genotype levels, which is likely to be related to the function of the encoded proteins and may determine key evolutionary traits of viruses, such as the level of genetic variation and host range. The diversity of codon adaptations at the genetic level in ASFV may account for differences in translational selection in ASFV hosts and provides insight into viral host adaptation and co-evolution.

Understanding the nucleotide composition and patterns of codon usage in the expression of human oral cancer genes

Oral squamous cell carcinoma (OSCC) is primarily known as oral cancer (OC) that mostly occurs in mouth, lips and tongue. Mutations in some of the genes cause OC and some genes are risk factors for progression of OC. In this study, we analyzed the compositional features and pattern of codon usage in genes involved in OC using computational method as no work was reported yet. Compositional features suggested that the overall GC content was higher i.e. genes were GC rich. Effective number of codons (ENC) values ranged from 34.6 to 55.9 with a mean value of 49.03±4.22 representing low codon usage bias (CUB). Correspondence analysis (COA) suggested that the codon usage pattern was different in different genes. In genes associated with OC, highly significant correlation was observed between GC12 and GC3 (r=0.454, p<0.01) suggesting that directional mutation affected all the three codon positions. This is the first report on pattern of codon usage pattern on genes involved in OC, which not only alludes a new perspective for elucidating the mechanisms of biased usage of synonymous codons but also provide valuable clues for molecular genetic engineering.

Codon usage bias of goose circovirus and its adaptation to host

Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes significant economic losses in the waterfowl industry. The codon usage patterns of viruses reflect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons (ENC) indicated a low overall extent of codon usage bias (CUB) in GoCV. Combined with the base composition and relative synonymous codon usage (RSCU) analysis, the results revealed a bias toward A- and G-ending codons in the overall codon usage. Analysis of the ENC-GC3s plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor influence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis (COA), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.

Comparative Analysis of Chloroplast Genomes in Cephaleuros and Its Related Genus (Trentepohlia): Insights into Adaptive Evolution

Cephaleuros species are well-known as plant pathogens that cause red rust or algae spot diseases in many economically cultivated plants that grow in shady and humid environments. Despite their prevalence, the adaptive evolution of these pathogens remains poorly understood. We sequenced and characterized three Cephaleuros (Cephaleuros lagerheimii, Cephaleuros diffusus, and Cephaleuros virescens) chloroplast genomes, and compared them with seven previously reported chloroplast genomes. The chloroplast sequences of C. lagerheimii, C. diffusus, and C. virescens were 480,613 bp, 383,846 bp, and 472,444 bp in length, respectively. These chloroplast genomes encoded 94 genes, including 27 tRNA genes, 3 rRNA genes, and 64 protein-coding genes. Comparative analysis uncovered that the variation in genome size was principally due to the length of intergenic spacer sequences, followed by introns. Furthermore, several highly variable regions (trnY-GTA, trnL-TAG, petA, psbT, trnD-GTC, trnL-TAA, ccsA, petG, psaA, psaB, rps11, rps2, and rps14) were identified. Codon bias analysis revealed that the codon usage pattern of Cephaleuros is predominantly shaped by natural selection. Additionally, six chloroplast protein-coding genes (atpF, chlN, psaA, psaB, psbA, and rbcL) were determined to be under positive selection, suggesting they may play a vital roles in the adaptation of Cephaleuros to low-light intensity habitats.

Genome-Wide Analysis of Serine Carboxypeptidase-like Genes in Soybean and Their Roles in Stress Resistance

The serine carboxypeptidase-like (SCPL) gene family plays a crucial role in the regulation of plant growth, development, and stress response through activities such as acyltransferases in plant secondary metabolism pathways. Although SCPL genes have been identified in various plant species, their specific functions and characteristics in soybean (Glycine max) have not yet been studied. We identified and characterized 73 SCPL genes, grouped into three subgroups based on gene structure and phylogenetic relationships. These genes are distributed unevenly across 20 soybean chromosomes and show varied codon usage patterns influenced by both mutation and selection pressures. Gene ontology (GO) enrichment suggests these genes are involved in plant cell wall regulation and stress responses. Expression analysis in various tissues and under stress conditions, including the presence of numerous stress-related cis-acting elements, indicated that these genes have varied expression patterns. This suggests that they play specialized roles such as modulating plant defense mechanisms against nematode infections, enhancing tolerance to drought and high salinity, and responding to cold stress, thereby helping soybean adapt to environmental stresses. Moreover, the expression of specific GmSCPLs was significantly affected following exposure to nematode infection, drought, high salt (NaCl), and cold stresses. Our findings underscore the potential of SCPL genes in enhancing stress resistance in soybean, providing a valuable resource for future genetic improvement and breeding strategies.

Codon usage bias of human papillomavirus type 33 and 58: A comprehensive analysis

Cervical cancer is closely linked to specific strains of human papillomavirus (HPV), notably HPV-33 and HPV-58, which exhibit a significant prevalence among women in China. Nevertheless, the codon usage bias in HPV-33 and HPV-58 is not well comprehended. The objective of this research is to analyze the codon usage patterns HPV-33 and HPV-58, pinpoint the primary factors that influence codon preference. The overall preference for codon usage in two HPV genotypes is not significant. Both HPV genotypes exhibit a preference for codons that end with A/U. The GC3 content for HPV-33 is 25.43% ± 0.35%, and for HPV-58, it is 29.44% ± 0.57%. Out of the 26 favored codons in HPV-33 and HPV-58 (relative synonymous codon usage (RSCU) > 1), 25 conclude with A/U. Principal component analysis (PCA) shows a tight clustering of the entire genome sequences of HPV-33 and HPV-58, suggesting a similarity in their RSCU preferences. Moreover, an examination of dinucleotide abundance indicated that translation selection influenced the development of a distinctive dinucleotide usage pattern in HPV-33 and HPV-58. Additionally, a combined analysis involving an effective number of codons plot, parity rule 2, and neutrality analysis demonstrated that, for HPV-33 and HPV-58, the primary determinant influencing codon usage preference is natural selection. HPV-33 and HPV-58 exhibit a restricted set of favored codons in common with humans, potentially mitigating competition for translation resources. Our discoveries could provide valuable perspectives on the evolutionary patterns and codon usage preferences of HPV-33 and HPV-58 viruses, contributing to the development and application of relevant HPV subtype vaccines.

Codon usage bias analysis in the mitochondrial genomes of five Rhingia Scopoli (Diptera, Syrphidae, Eristalinae) species

This study presents the sequencing and annotation of mitochondrial genomes from five Rhingia species of the family Syrphidae, focusing on codon bias. Each species possessed 22 tRNAs genes, 13 protein-coding genes, 2 rRNAs genes, and a control region, without any observed gene rearrangements. Nucleotide composition analysis revealed a higher AT content compared with GC content, indicating AT enrichment. Neutrality plot, Parity rule 2 bias, and effective number of codons plot analyses collectively indicated that natural selection primarily influences the codon usage bias in the five Rhingia species. Relative synonymous codon usage analysis identified the optimal codons for Rhingia binotata, R. fromosana, R. campestris, R. louguanensis, and R. xanthopoda as 10, 14, 10, 11, and 12, respectively, all ending with A/U and exhibiting AT preference. Phylogenetic analysis, based on maximum likelihood and Bayesian inference methods applied to three datasets, confirmed the monophyly of Rhingia. In conclusion, this research establishes a foundation for understanding the phylogenetic evolution and codon usage patterns in Rhingia, offering valuable for future studies.

Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases

Mitochondrial dysfunction is the leading cause of neurodegenerative disorders like Alzheimer's disease and Parkinson's disease. Mitochondria is a highly dynamic organelle continuously undergoing the process of fission and fusion for even distribution of components and maintaining proper shape, number, and bioenergetic functionality. A set of genes governs the process of fission and fusion. OPA1, Mfn1, and Mfn2 govern fusion, while Drp1, Fis1, MIEF1, and MIEF2 genes control fission. Determination of specific molecular patterns of transcripts of these genes revealed the impact of compositional constraints on selecting optimal codons. AGA and CCA codons were over-represented, and CCC, GTC, TTC, GGG, ACG were under-represented in the fusion gene set. In contrast, CTG was over-represented, and GCG, CCG, and TCG were under-represented in the fission gene set. Hydropathicity analysis revealed non-polar protein products of both fission and fusion gene set transcripts. AGA codon repeats are an integral part of translational regulation machinery and present a distinct pattern of over-representation and under-representation in different transcripts within the gene sets, suggestive of selective translational force precisely controlling the occurrence of the codon. Out of six synonymous codons, five synonymous codons encoding for leucine were used differently in both gene sets. Hence, forces regulating the occurrence of AGA and five synonymous leucine-encoding codons suggest translational selection. A correlation of mutational bias with gene expression and codon bias and GRAVY and AROMA signifies the selection pressure in both gene sets, while the correlation of compositional bias with gene expression, codon bias, protein properties, and minimum free energy signifies the presence of compositional constraints. More than 25% of codons of both gene sets showed a significant difference in codon usage. The overall analysis shed light on molecular features of gene sets involved in fission and fusion.

Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species

Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference. The cluster analysis and phylogenetic analysis show that the differentiation relationship of them is different and indicate that codons with weak or unbiased preferences may also play an irreplaceable role in these species' evolution. In addition, we identified 26 common high-frequency codons and 8-18 optimal codons all ending in A/U in these 36 species. Our results will not only contribute to carrying out transgenic work in Gracilariaceae species to maximize the protein yield in the future, but also lay a theoretical foundation for further exploring systematic classification of them.

Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes

Leguminosae is one of the three largest families of angiosperms after Compositae and Orchidaceae. It is widely distributed and grows in a variety of environments, including plains, mountains, deserts, forests, grasslands, and even waters where almost all legumes can be found. It is one of the most important sources of starch, protein and oil in the food of mankind and also an important source of high-quality forage material for animals, which has important economic significance. In our study, the codon usage patterns and variation sources of the chloroplast genome of nine important forage legumes were systematically analyzed. Meanwhile, we also constructed a phylogenetic tree based on the whole chloroplast genomes and protein coding sequences of these nine forage legumes. Our results showed that the chloroplast genomes of nine forage legumes end with A/T bases, and seven identical high-frequency (HF) codons were detected among the nine forage legumes. ENC-GC3s mapping, PR2 analysis, and neutral analysis showed that the codon bias of nine forage legumes was influenced by many factors, among which natural selection was the main influencing factor. The codon usage frequency showed that the Nicotiana tabacum and Saccharomyces cerevisiae can be considered as receptors for the exogenous expression of chloroplast genes of these nine forage legumes. The phylogenetic relationships of the chloroplast genomes and protein coding genes were highly similar, and the nine forage legumes were divided into three major clades. Among the clades Melilotus officinalis was more closely related to Medicago sativa, and Galega officinalis was more closely related to Galega orientalis. This study provides a scientific basis for the molecular markers research, species identification and phylogenetic studies of forage legumes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01421-0.

Speciation, natural selection, and networks: three historians versus theoretical population geneticists

In 1913, the geneticist William Bateson called for a halt in studies of genetic phenomena until evolutionary fundamentals had been sufficiently addressed at the molecular level. Nevertheless, in the 1960s, the theoretical population geneticists celebrated a "modern synthesis" of the teachings of Mendel and Darwin, with an exclusive role for natural selection in speciation. This was supported, albeit with minor reservations, by historians Mark Adams and William Provine, who taught it to generations of students. In subsequent decades, doubts were raised by molecular biologists and, despite the deep influence of various mentors, Adams and Provine noted serious anomalies and began to question traditional "just-so-stories." They were joined in challenging the genetic orthodoxy by a scientist-historian, Donald Forsdyke, who suggested that a "collective variation" postulated by Darwin's young research associate, George Romanes, and a mysterious "residue" postulated by Bateson, might relate to differences in short runs of DNA bases (oligonucleotides). The dispute between a small network of historians and a large network of geneticists can be understood in the context of national politics. Contrasts are drawn between democracies, where capturing the narrative makes reversal difficult, and dictatorships, where overthrow of a supportive dictator can result in rapid reversal.

Novel Plastid Genome Characteristics in Fugacium kawagutii and the Trend of Accelerated Evolution of Plastid Proteins in Dinoflagellates

Typical (peridinin-containing) dinoflagellates possess plastid genomes composed of small plasmids named "minicircles". Despite the ecological importance of dinoflagellate photosynthesis in corals and marine ecosystems, the structural characteristics, replication dynamics, and evolutionary forcing of dinoflagellate plastid genomes remain poorly understood. Here, we sequenced the plastid genome of the symbiodiniacean species Fugacium kawagutii and conducted comparative analyses. We identified psbT-coding minicircles, features previously not found in Symbiodiniaceae. The copy number of F. kawagutii minicircles showed a strong diel dynamics, changing between 3.89 and 34.3 copies/cell and peaking in mid-light period. We found that F. kawagutii minicircles are the shortest among all dinoflagellates examined to date. Besides, the core regions of the minicircles are highly conserved within genus in Symbiodiniaceae. Furthermore, the codon usage bias of the plastid genomes in Heterocapsaceae, Amphidiniaceae, and Prorocentraceae species are greatly influenced by selection pressure, and in Pyrocystaceae, Symbiodiniaceae, Peridiniaceae, and Ceratiaceae species are influenced by both natural selection pressure and mutation pressure, indicating a family-level distinction in codon usage evolution in dinoflagellates. Phylogenetic analysis using 12 plastid-encoded proteins and five nucleus-encoded plastid proteins revealed accelerated evolution trend of both plastid- and nucleus-encoded plastid proteins in peridinin- and fucoxanthin-dinoflagellate plastids compared to plastid proteins of nondinoflagellate algae. These findings shed new light on the structure and evolution of plastid genomes in dinoflagellates, which will facilitate further studies on the evolutionary forcing and function of the diverse dinoflagellate plastids. The accelerated evolution documented here suggests plastid-encoded sequences are potentially useful for resolving closely related dinoflagellates.

Codon Pattern and Context Analysis in Genes Triggering Alzheimer's Disease and Latent Tau Protein Aggregation Post-Anesthesia Exhibited Unique Molecular Patterns Associated with Functional Aspects

Background

Previous reports have demonstrated post-operative dementia and Alzheimer's disease (AD), and increased amyloid-β levels and tau hyperphosphorylation have been observed in animal models post-anesthesia.

Objective

After surgical interventions, loss in memory has been observed that has been found linked with genes modulated after anesthesia. Present study aimed to study molecular pattern present in genes modulated post anesthesia and involved in characters progressing towards AD.

Methods

In the present study, 17 transcript variants belonging to eight genes, which have been found to modulate post-anesthesia and contribute to AD progression, were envisaged for their compositional features, molecular patterns, and codon and codon context-associated studies.

Results

The sequences' composition was G/C rich, influencing dinucleotide preference, codon preference, codon usage, and codon context. The G/C nucleotides being highly occurring nucleotides, CpGdinucleotides were also preferred; however, CpG was highly disfavored at p3-1 at the codon junction. The nucleotide composition of Cytosine exhibited a unique feature, and unlike other nucleotides, it did not correlate with codon bias. Contrarily, it correlated with the sequence lengths. The sequences were leucine-rich, and multiple leucine repeats were present, exhibiting the functional role of neuroprotection from neuroinflammation post-anesthesia.

Conclusions

The analysis pave the way to elucidate unique molecular patterns in genes modulated during anesthetic treatment and might help ameliorate the ill effects of anesthetics in the future.

Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype

African swine fever (ASF) is a severe haemorrhagic disease caused by the African swine fever virus (ASFV), transmitted by ticks, resulting in high mortality among domestic pigs and wild boars. The global spread of ASFV poses significant economic threats to the swine industry. This study employs diverse analytical methods to explore ASFV's evolution and host adaptation, focusing on codon usage patterns and associated factors. Utilizing phylogenetic analysis methods including neighbour-joining and maximum-likelihood, 64 ASFV strains were categorized into four clades. Codon usage bias (CUB) is modest in ASFV coding sequences. This research identifies multiple factors - such as nucleotide composition, mutational pressures, natural selection and geographical diversity - contributing to the formation of CUB in ASFV. Analysis of relative synonymous codon usage reveals CUB variations within clades and among ASFVs and their hosts. Both Codon Adaptation Index and Similarity Index analyses confirm that ASFV strains are highly adapted to soft ticks (Ornithodoros moubata) but less so to domestic pigs, which could be a result of the long-term co-evolution of ASFV with ticks. This study sheds light on the factors influencing ASFV's codon usage and fitness dynamics, enriching our understanding of its evolution, adaptation and host interactions.

Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species

Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.

Chargaff's second parity rule lies at the origin of additive genetic interactions in quantitative traits to make omnigenic selection possible

Background

Francis Crick's central dogma provides a residue-by-residue mechanistic explanation of the flow of genetic information in living systems. However, this principle may not be sufficient for explaining how random mutations cause continuous variation of quantitative highly polygenic complex traits. Chargaff's second parity rule (CSPR), also referred to as intrastrand DNA symmetry, defined as near-exact equalities G ≈ C and A ≈ T within a single DNA strand, is a statistical property of cellular genomes. The phenomenon of intrastrand DNA symmetry was discovered more than 50 years ago; at present, it remains unclear what its biological role is, what the mechanisms are that force cellular genomes to comply strictly with CSPR, and why genomes of certain noncellular organisms have broken intrastrand DNA symmetry. The present work is aimed at studying a possible link between intrastrand DNA symmetry and the origin of genetic interactions in quantitative traits.

Methods

Computational analysis of single-nucleotide polymorphisms in human and mouse populations and of nucleotide composition biases at different codon positions in bacterial and human proteomes.

Results

The analysis of mutation spectra inferred from single-nucleotide polymorphisms observed in murine and human populations revealed near-exact equalities of numbers of reverse complementary mutations, indicating that random genetic variations obey CSPR. Furthermore, nucleotide compositions of coding sequences proved to be statistically interwoven via CSPR because pyrimidine bias at the 3rd codon position compensates purine bias at the 1st and 2nd positions.

Conclusions

According to Fisher's infinitesimal model, we propose that accumulation of reverse complementary mutations results in a continuous phenotypic variation due to small additive effects of statistically interwoven genetic variations. Therefore, additive genetic interactions can be inferred as a statistical entanglement of nucleotide compositions of separate genetic loci. CSPR challenges the neutral theory of molecular evolution-because all random mutations participate in variation of a trait-and provides an alternative solution to Haldane's dilemma by making a gene function diffuse. We propose that CSPR is symmetry of Fisher's infinitesimal model and that genetic information can be transferred in an implicit contactless manner.

The evolutionary characterization of Gamasida based on mitochondrial genes codon usage pattern

Mites belonging to the suborder Gamasida are species-rich and habitat-diverse, with a worldwide distribution. To adapt to the environment and obtain better living conditions, all species of the suborder Gamasida have been undergoing constant evolution. The complete mitochondrial genome (mitogenome) is an invaluable molecular marker for studying the origin of species, genetic differentiation between closely related species, and between intraspecific groups. In some species of the suborder Gamasida, mitochondrial tRNA genes are truncated and carried unstable genetic information. This study presents a comparative analysis of codon usage pattern and preference of 13 protein-coding genes of 24 species in 17 genera and 10 families of the suborder Gamasida. Results showed that have an obvious AT preference (0.664-0.829) for codon usage in the suborder Gamasida. Most of the optimal and high-frequency codons also end in A/T. The degree of natural selection varies between the same protein-coding genes of different gamasid mites or among different protein-coding genes within the same gamasid mites. Base and codon usage pattern and preference are very similar between the same species and genus, namely the closer species, the more similar their bases and codons usage patterns and preference are. T bases and C bases were the preference bases for codon usage of 24 species in the suborder Gamasida. Evolution of the suborder Gamasida was dominated by natural selection (64.1%). This study provides the first comprehensive analysis of codon usage in the suborder Gamasida, which will greatly improve our understanding of codon usage patterns and preference, genetics, and evolution of the suborder Gamasida. It will help to evaluate the degree of molecular adaptation in the suborder Gamasida and to further explore evolutionary features of the suborder Gamasida.

Comparative Genomics Reveals Three Genetic Groups of the Whitefly Obligate Endosymbiont Candidatus Portiera aleyrodidarum

Maternally inherited obligate endosymbionts codiverge with their invertebrate hosts and reflect their host's evolutionary history. Whiteflies (Hemiptera: Aleyrodidae) harbor one obligate endosymbiont, Candidatus Portiera aleyrodidarum (hereafter Portiera). Portiera was anciently acquired by whitefly and has been coevolving with its host ever since. Uncovering the divergence of endosymbionts provides a fundamental basis for inspecting the coevolutionary processes between the bacteria and their hosts. To illustrate the divergence of Portiera lineages across different whitefly species, we sequenced the Portiera genome from Aleyrodes shizuokensis and conducted a comparative analysis on the basic features and gene evolution with bacterial genomes from five whitefly genera, namely Aleurodicus, Aleyrodes, Bemisia, Pealius, and Trialeurodes. The results indicated that Portiera from Bemisia possessed significantly larger genomes, fewer coding sequences (CDSs), and a lower coding density. Their gene arrangement differed notably from those of other genera. The phylogeny of the nine Portiera lineages resembled that of their hosts. Moreover, the lineages were classified into three distinct genetic groups based on the genetic distance, one from Aleurodicus (Aleurodicinae), one from Bemisia (Aleyrodinae), and another from Aleyrodes, Pealius, and Trialeurrodes (Aleyrodinae). Synonymous and nonsynonymous rate analyses, parity rule 2 plot analyses, neutrality plot analyses, and effective number of codons analyses supported the distinction of the three genetic groups. Our results indicated that Portiera from distant hosts exhibit distinct genomic contents, implying codivergence between hosts and their endosymbionts. This work will enhance our understanding of coevolution between hosts and their endosymbionts.

Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias

Rabies virus (RABV) is a highly pathogenic virus that causes a fatal disease in humans and other mammals, but the mechanism of its evolution, spread, and spillover remains unknown. In this study, we analyzed the codon usage pattern of 2,018 RABV full-length genome sequences from 79 countries collected between 1931 and 2021 to provide an insight into its molecular evolution and unravel its unknown host-adapted pattern. We found that RABV exhibited a weak codon usage bias, with a preference for the codons ending in A (28.10 ± 0.01) or U (26.43 ± 0.02). Moreover, natural selection plays a major role in shaping the codon usage bias of the RABV. Notably, nearly half of the 18 codons in the virus were best matched to the hosts' most abundant isoacceptor tRNAs, which might account for the wide range of RABV hosts. Furthermore, significant differences were observed in the codon usage patterns of RABV for different host species, suggesting that codon usage bias may be influenced by host-specific factors. In conclusion, our study reveals codon usage patterns of RABV that may help in the development of control strategies and effective vaccines and therapies against this deadly virus.

Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of Invertebrate iridescent virus 6

The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favored in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Japanagallia is a genus of Cicadomorpha in the family of leafhoppers that are plant piercing-sucking insects, and it is difficult to distinguish by morphological characteristics. So far, only one complete mitochondrial genome data has been reported for the genus Japanagallia. Therefore, in order to better understand this group, we assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. Nucleotide composition analysis showed that AT content was higher than GC content, and the protein-coding sequences preferred to end with A/T at the third codon position. Relative synonymous codon usage analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed the codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure. In the neutrality plot, the slopes of regression lines were < 0.5, suggesting that natural selection was playing a major role while mutation pressure was of minor importance. The effective number of codons showed that the codon usage bias between genes and genomes was low. Correspondence analysis revealed that the codon usage pattern differed among 13 protein-coding genes. Phylogenetic analyses based on three datasets using two methods (maximum likelihood and Bayesian inference), restored the Megophthalminae monophyly with high support values (bootstrap support values (BS) = 100, Bayesian posterior probability (PP) = 1). In the obtained topology, the seven Japanagallia species were clustered into a monophyletic group and formed a sister group with Durgade. In conclusion, our study can provide a reference for the future research on organism evolution, identification and phylogeny relationships of Japanagallia species.

Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule

Chargaff's second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

BACKGROUND

The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation.

RESULTS

Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes.

CONCLUSION

This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code

Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson-Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons' relationship as to how to develop the DNA molecule on the principle of Watson-Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system.

Structural Characteristics of Mitochondrial Genomes of Eight Treehoppers (Hemiptera: Membracidae: Centrotinae) and Their Phylogenetic Implications

Complete mitochondrial genomes were newly sequenced for eight species of the treehopper subfamily Centrotinae (Hemiptera: Membracidae), four of which represent genera for which mitogenomes were not previously available. The new mitogenomes are generally similar in overall structure, gene order, base composition, and nucleotide content to those of previously sequenced species of the subfamily. Phylogenetic analyses were conducted using both maximum likelihood and Bayesian inference methods based on three separate nucleotide sequence datasets in which RNA gene sequences and/or third codon positions were either included or excluded from the concatenated protein-coding gene alignments. The results are consistent with previous phylogenies based on morphology and partial nuclear genome data, except for the lack of support for the monophyly of Leptocentrini. These results show that mitogenome sequences are informative of both ancient and recent divergence patterns within Centrotinae.

Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa

Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.

Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae)

Krisna species are insects that have piercing-sucking mouthparts and belong to the Krisnini tribe in the Iassinae subfamily of leafhoppers in the Cicadellidae family. In this study, we sequenced and compared the mitochondrial genomes (mitogenomes) of four Krisna species. The results showed that all four mitogenomes were composed of cyclic double-stranded molecules and contained 13 protein-coding genes (PCGs) and 22 and 2 genes coding for tRNAs and rRNAs, respectively. Those mitogenomes exhibited similar base composition, gene size, and codon usage patterns for the protein-coding genes. The analysis of the nonsynonymous substitution rate (Ka)/synonymous substitution rate (Ks) showed that evolution occurred the fastest in ND4 and the slowest in COI. 13 PCGs that underwent purification selection were suitable for studying phylogenetic relationships within Krisna. ND2, ND6, and ATP6 had highly variable nucleotide diversity, whereas COI and ND1 exhibited the lowest diversity. Genes or gene regions with high nucleotide diversity can provide potential marker candidates for population genetics and species delimitation in Krisna. Analyses of parity and neutral plots showed that both natural selection and mutation pressure affected the codon usage bias. In the phylogenetic analysis, all subfamilies were restored to a monophyletic group; the Krisnini tribe is monophyletic, and the Krisna genus is paraphyletic. Our study provides novel insights into the significance of the background nucleotide composition and codon usage patterns in the CDSs of the 13 mitochondrial PCGs of the Krisna genome, which could enable the identification of a different gene organization and may be used for accurate phylogenetic analysis of Krisna species.