Patterns Of Codon Usage Bias Research Articles

Genetic analysis of tomato brown rugose fruit virus reveals evolutionary adaptation and codon usage bias patterns

Tomato brown rugose fruit virus (ToBRFV) poses a significant threat to tomato production worldwide, prompting extensive research into its genetic diversity, evolutionary dynamics, and adaptive strategies. In this study, we conducted a comprehensive analysis of ToBRFV at the codon level, focusing on codon usage bias, selection pressures, and evolutionary patterns across multiple genes. Our analysis revealed distinct patterns of codon usage bias and selection pressures within the ToBRFV genome, with varying levels of genetic diversity and evolutionary constraints among different genes. We observed a transition/transversion bias of 2.07 across the entire ToBRFV genome, with the movement protein (MP) gene exhibiting the highest transition/transversion bias and SNP density, suggesting potential evolutionary pressures or a higher mutation rate in this gene. Furthermore, our study identified episodic positive selection primarily in the MP gene, highlighting specific codons subject to adaptive changes in response to host immune pressures or environmental factors. Comparative analysis of codon usage bias in the coat protein (CP) and RNA-dependent RNA polymerase (RdRp) genes revealed gene-specific patterns reflecting functional constraints and adaptation to the host's translational machinery. Our findings provide valuable insights into the molecular mechanisms driving ToBRFV evolution and adaptation, with implications for understanding viral pathogenesis, host-virus interactions, and the development of control strategies. Future research directions include further elucidating the functional significance of codon usage biases, exploring the role of episodic positive selection in viral adaptation, and leveraging these insights to inform the development of effective antiviral strategies and crop protection measures.

Identification and Genomic Characterization of Two Novel Hepatoviruses in Shrews from Yunnan Province, China.

Hepatitis A virus (HAV), a member of the genus Hepatovirus (Picornaviridae HepV), remains a significant viral pathogen, frequently causing enterically transmitted hepatitis worldwide. In this study, we conducted an epidemiological survey of HepVs carried by small terrestrial mammals in the wild in Yunnan Province, China. Utilizing HepV-specific broad-spectrum RT-PCR, next-generation sequencing (NGS), and QNome nanopore sequencing (QNS) techniques, we identified and characterized two novel HepVs provisionally named EpMa-HAV and EpLe-HAV, discovered in the long-tailed mountain shrew (Episoriculus macrurus) and long-tailed brown-toothed shrew (Episoriculus leucops), respectively. Our sequence and phylogenetic analyses of EpMa-HAV and EpLe-HAV indicated that they belong to the species Hepatovirus I (HepV-I) clade II, also known as the Chinese shrew HepV clade. Notably, the codon usage bias pattern of novel shrew HepVs is consistent with that of previously identified Chinese shrew HepV. Furthermore, our structural analysis demonstrated that shrew HepVs differ from other mammalian HepVs in RNA secondary structure and exhibit variances in key protein sites. Overall, the discovery of two novel HepVs in shrews expands the host range of HepV and underscores the existence of genetically diverse animal homologs of human HAV within the genus HepV.

Comparative Study on Codon Usage Patterns across Chloroplast Genomes of Eighteen Taraxacum Species

This study investigates codon usage bias within the chloroplast genomes of 18 Taraxacum species, focusing on the base composition and various metrics including GC content, Relative Synonymous Codon Usage (RSCU), Effective Number of Codons (ENc), and GC3s. Our analysis revealed a pronounced preference for A/T-ending codons across Taraxacum species, with GC content across the first, second, and third positions of the codons (GC1, GC2, GC3) and the average GC content consistently below 50%. A detailed examination using the RSCU metric identified 29 commonly preferred A/T-ending codons, indicating a strong codon usage bias towards these endings. Specifically, the codon for leucine (UUA) emerged as highly preferred, while the codon for serine (AGC) was least favored. Through the ENc–GC3s plot analysis, we explored the forces shaping this bias, finding evidence that both mutation pressure and natural selection significantly influence codon preference, with most coding sequences showing weak bias. The PR2 plot analysis further confirmed the role of these factors by demonstrating a higher frequency of T over A and C over G at the third codon position, pointing towards a mutation bias complemented by natural selection. Collectively, our findings highlight a consistent pattern of codon usage bias in the chloroplast genomes of Taraxacum species, influenced by a combination of mutation pressure, natural selection, and possibly other unidentified factors.

Comprehensive examination on codon usage bias pattern of the Bovine Ephemeral fever virus

Bovine Ephemeral Fever Virus (BEFV) is a non-contagious virus that commonly infects cattle and water buffalo, reduces milk productivity, decreases the quality of beef, and causes an adverse economic impact on the global livestock industry. However, the evolution of BEFV is unclear, and uncertainty exists regarding its global geodynamics. Consequently, this study aims to comprehend the pattern of viral evolution and gene expression in the BEFV genes G, M, N, and P, including synonymous codons. Additionally, we performed recombination analyses, which exclusively detected recombination signals in the G- and P-genes. Subsequently, a phylogenetic tree was constructed to validate and support these findings. The codon usage bias results showed that the BEFV-selected genes were influenced by both natural and mutation pressure. Furthermore, nucleotide A is more abundant in all the selected genes. The eNC values, ranging from 42.99 to 47.10, revealed the presence of moderate codon usage bias, where gene P exhibited the highest and gene G had the lowest codon usage bias. The neutrality and PR-2 plots, specified codon usage patterns of the genes, are also being shaped by strong selectional pressure. This comprehensive analysis of BEFV genes (G, M, N, and P) sheds light on the molecular evolutionary patterns, co-adaptation, and different genes expression in diverse regions, facilitating the development of preventative programs and insights into viral pathogenesis and vaccine design. Communicated by Ramaswamy H. Sarma

Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions.

Bacteriophages are being widely harnessed as an alternative to antibiotics due to the global emergence of drug-resistant pathogens. To guide the usage of these bactericidal agents, characterization of their host specificity is vital-however, host range information remains limited for many bacteriophages. This is particularly the case for bacteriophages infecting the Microbacterium genus, despite their importance in agriculture, biomedicine, and biotechnology. Here, we elucidate the phylogenomic relationships between 125 Microbacterium cluster EA bacteriophages-including members from 11 sub-clusters (EA1 to EA11)-and infer their putative host ranges using insights from codon usage bias patterns as well as predictions from both exploratory and confirmatory computational methods. Our computational analyses suggest that cluster EA bacteriophages have a shared infection history across the Microbacterium clade. Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. Furthermore, host range predictions indicate that certain sub-clusters may be better suited in prospective biotechnological and medical applications such as phage therapy.

Unexpected absence of ribosomal protein genes from metagenome-assembled genomes

Metagenome-assembled genomes (MAGs) have revealed the hidden diversity and functions of uncultivated microbes, but their reconstruction from metagenomes remains a computationally difficult task. Repetitive or exogenous sequences, such as ribosomal RNA and horizontally transferred genes, are frequently absent from MAGs because of misassembly and binning errors. Here, we report that ribosomal protein genes are also often absent from MAGs, although they are neither repetitive nor exogenous. Comprehensive analyses of more than 190,000 MAGs revealed that these genes could be missing in more than 20–40% of near-complete (i.e., with completeness of 90% or higher) MAGs. While some uncultivated environmental microbes intrinsically lack some ribosomal protein genes, we found that this unexpected absence is largely due to special evolutionary patterns of codon usage bias in ribosomal protein genes and algorithmic characteristics of metagenomic binning, which is dependent on tetranucleotide frequencies of contigs. This problem reflects the microbial life-history strategy. Fast-growing microbes tend to have this difficulty, likely because of strong evolutionary pressures on ribosomal protein genes toward the efficient assembly of ribosomes. Our observations caution those who study genomics and phylogeny of uncultivated microbes, the diversity and evolution of microbial genes in the central dogma, and bioinformatics in metagenomics.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi.

Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host-pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host-pathogen interactions through genome editing and functional genomics tools.

Re-evaluating Loricate Choanoflagellate Phylogenetics: Molecular Evidence Points to the Paraphyly of Tectiform Species

Lorica-bearing choanoflagellates belong to the order Acanthoecida, a taxon which has been consistently recovered as monophyletic in molecular phylogenies. Based upon differences in lorica development and morphology, as well as the presence or absence of a motile dispersal stage, species are labelled as either nudiform or tectiform. Whilst Acanthoecida is robustly resolved in molecular phylogenies, the placement of the root of the clade is less certain with two different positions identified in past studies. One recovered root has been placed between the nudiform family Acanthoecidae and the tectiform family Stephanoecidae. An alternative root placement falls within the tectiform species, recovering the monophyletic Acanthoecidae nested within a paraphyletic Stephanoecidae. Presented here is a 14-gene phylogeny, based upon nucleotide and amino acid sequences, which strongly supports tectiform paraphyly. The horizontal transfer of a ribosomal protein gene, from a possible SAR donor, into a subset of acanthoecid species provides further, independent, support for this root placement. Differing patterns of codon usage bias across the choanoflagellates are proposed as the cause of artefactual phylogenetic signals that lead to the recovery of tectiform monophyly.

Variation of natural selection in the Amoebozoa reveals heterogeneity across the phylogeny and adaptive evolution in diverse lineages.

The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial role in understanding the evolution of the supergroup. In this study, we searched for traces of natural selection based on a set of highly conserved protein-coding genes in a phylogenetic framework from a broad sampling of amoebozoans. Using these genes, we estimated substitution rates and inferred patterns of selective pressure in lineages and sites with various models. We also examined the effect of selective pressure on codon usage bias and potential correlations with observed biological traits and habitat. Results showed large heterogeneity of selection across lineages of Amoebozoa, indicating potential species-specific optimization of adaptation to their diverse ecological environment. Overall, lineages in Tubulinea had undergone stronger purifying selection with higher average substitution rates compared to Discosea and Evosea. Evidence of adaptive evolution was observed in some representative lineages and in a gene (Rpl7a) within Evosea, suggesting potential innovation and beneficial mutations in these lineages. Our results revealed that members of the fast-evolving lineages, Entamoeba and Cutosea, all underwent strong purifying selection but had distinct patterns of codon usage bias. For the first time, this study revealed an overall pattern of natural selection across the phylogeny of Amoebozoa and provided significant implications on their distinctive evolutionary processes.

Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade.

Enterovirus A (EV-A) species cause hand, foot and mouth disease (HFMD), threatening the health of young children. Understanding the mutual codon usage pattern of the virus and its host(s) has fundamental and applied values. Here, through examining multiple codon usage parameters, we found that the codon usage bias among EV-A strains varies and is clade-specific. EVA76, EVA89, EVA90, EVA91 and EVA92, the unconventional clade of EV-A strains, show unique codon usage pattern relative to the two conventional clades, including EVA71, CVA16, CVA6 and CVA10, etc. Analyses of Effective Number of Codon (ENC), Correspondence Analysis (COA) and Parity Rule 2 (PR2), etc., revealed that the codon usage patterns of EV-A strains are shaped by mutation pressure and natural selection. Based on the neutrality analysis, we determined the dominant role of natural selection in the formation of the codon usage bias of EV-A. In addition, we have determined the codon usage compatibility of potential hosts for EV-A strains using codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses, and found that EV-A showed host-specific codon adaptation patterns in different clades. Finally, we confirmed that the unique codon usage pattern of the unconventional clade affected protein expression level in human cell lines. In conclusion, we identified novel characteristics of codon usage bias in distinct EV-A clades associated with their host range, transmission and pathogenicity.

Plastome evolution of Aeonium and Monanthes (Crassulaceae): insights into the variation of plastomic tRNAs, and the patterns of codon usage and aversion.

This study reported 13 new plastomes from Aeonium and Monanthes, and observed new markers for phylogeny and DNA barcoding, such as novel tRNA structures and codon usage bias and aversion. The Macaronesian clade of Crassulaceae consists of three genera: Aichryson, with about 15 species; Monanthes, with about 10 species; Aeonium, with about 40 species. Within this clade, Aeonium, known as "the botanical equivalent of Darwin's finches", is regarded as an excellent model plant for researching adaptive evolution. Differing from the well-resolved relationships among three genera of the Macaronesian clade, the internal branching patterns within the genus Aeonium are largely unclear. In this study, we first reported 13 new plastomes from genus Aeonium and the closely related genus Monanthes. We further performed comprehensive analyses of the plastomes, with focuses on the secondary structures of pttRNAs and the patterns of codon usage and aversion. With a typical circular and quadripartite structure, the 13 plastomes ranged from 149,900 to 151,030bp in size, and the unique pattern in IR junctions might become a family-specific marker for Crassulaceae species. Surprisingly, the π values of plastomes from Monanthes were almost twice those from Aeonium. Most importantly, we strongly recommend that highly polymorphic regions, novel putative pttRNA structures, patterns of codon usage bias and aversion derived from plastomes might have phylogenetic implications, and could act as new markers for DNA barcoding of plants. The results of phylogenetic analyses strongly supported a clear internal branching pattern in Macaronesian clade (represented by Aeonium and Monanthes), with higher nodal support values. The findings reported here will provide new insights into the variation of pttRNAs, and the patterns of codon usage and aversion of the family Crassulaceae.

Comparative studies of codon usage profile of Anisakis simplex (Nematoda) and Carassius gibelio (Prussian carp)

Aim: The aim of the present study was to understand the molecular relationship between nematode (parasite) and fish (host) through codon usage bias (CUB) analysis. Methodology: The Codon usage bias analysis has been performed in fish Carassius gibelio (Prussian carp) and nematode fish parasite Anisakis simplex. The complete coding sequences (CDS) of C. gibelio (Prussian carp) and A. simplex (Nematode) were retrieved from National Center for Biotechnology Information and followed to that we have performed bioinformatics analysis to understand the codon usage pattern between host and parasite. Results: Different CUB indices like Relative synonymous codon usage (RSCU), Effective number of codons (ENC), Codon adaptation index (CAI) and Codon bias index (CBI) revealed a similar pattern in the codon usage in C. gibelio and A. simplex. In addition, inclusive analysis using different plots (ENC, parity, neutrality) had shown the influence of both the evolutionary forces i.e mutational and translational selection on codon usage pattern. This describes the role of evolutionary forces in determining the conserved genome to establish species-specific function-level differences for efficient survival. Interpretation: The present study elucidated the association between Carassiusgibelio (host) and Anisakis simplex (parasite) based on the similar pattern of codon usage bias between both the species.

Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5'-ends to the 3'-ends.

Brachypodium distachyon, a new monocotyledonous model plant, has received wide attention in biological research due to its small genome and numerous genetic resources. Codon usage bias is an important feature of genes and genomes, and it can be used in transgenic and evolutionary studies. In this study, the nucleotide compositions and patterns of codon usage bias were calculated using Codon W. Additionally, an ENC plot, Parity rule 2 and correspondence analyses were used to explore the major factors influencing codon usage bias patterns. The numbers of hydrogen bonds and skews were used to analyze the GC trend in the 5′-ends of the coding sequences. The results showed that minor differences in the codon usage bias patterns were revealed by the ENC plot, Parity rule 2 and correspondence analyses. The analyses of the CG-skew and the number of hydrogen bonds showed a declining trend in the number of cytosines at the 5′-ends of the CDSs (from the 5′-ends to the 3′-ends), indicating that GC may play a major role in codon usage bias. In addition, our results laid a foundation for the study of codon usage bias patterns in Brachypodium genus and suggested that the GC plays a major role in determining these patterns.

Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia.

The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.

Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections but also offering novel insights into pathogen genetics and evolution. A prominent example is cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative nonpathogenic relatives, such as Mycobacterium smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate subcluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with Mycobacterium leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, subcluster K1 mycobacteriophages are able to integrate into the genomes of Mycobacterium abscessus and Mycobacterium marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance.

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.

Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications.

Dipelta (Caprifoliaceae) is a Tertiary relict genus endemic to China, comprising three species with horticultural and medicinal values. For the lack of genomic information, interspecific relationships and divergence times in the genus remain unresolved. In the present study, we assembled and characterized the complete plastomes, the partial mitogenomes, and nuclear internal transcribed spacer (ITS) fragments from genome skimming datasets of 14 Dipelta individuals. The plastomes were conserved in genomic structure, gene order, and gene content, but with highly variable repeat sequences. Three genes (rpl23, ycf1, ycf2) were examined with positive selection, and nine divergent hotpot regions (psbL, accD, rpl23, ycf2, ycf3, rbcL-accD, trnI-CAU-ycf2, ndhH-rps15, and rps18 intron) were potentially valuable for DNA barcodes. Contrasted to the variability in plastome sequences, mitogenomes contained 12 protein-coding genes with limited indels and nucleotide substitutions, and no gene was found under positive selection. Genes in organellar genomes tended to have a similar pattern of codon usage bias, with a preference of A/U ending codons. Phylogenetic trees constructed with plastomes, mitogenomes, and ITS sequences consistently supported that Dipelta was monophyletic, and Dipelta elegans was sister to the other two taxa. Interspecific divergences were estimated at about 33–37 Ma in the Eocene/Oligocene boundary, suggesting the paleo-endemism of the extant species as “living fossils” of the East Asian Flora. Our study well-exhibited that genome skimming could provide valuable genomic information to elucidate the evolutionary history of the complex group in a cost-efficient way.

Codon usage pattern and its influencing factors for mitochondrial CO genes among different classes of Arthropoda

Analysis of codon usage bias (CUB) is very much important in perceiving the knowledge of molecular biology, the discovery of a new gene, designing of transgenes and evolution of gene. In this study, we analyzed compositional features and codon usage of MT-CO (COI, COII and COIII) genes among the classes of Arthropoda to explore the pattern of CUB as no research work was reported yet. Nucleotide composition analysis in CO genes suggested that the genes were AT-rich in all the four classes of Arthropoda. CUB was low in all the classes of Arthropoda for MT-CO genes as revealed from a high effective number of codons (ENC). We also found that the evolutionary forces namely mutation pressure and natural selection were the key influencing factors in CUB among MT-CO genes as revealed by correlation analysis between overall nucleotide composition and nucleotide composition at the 3rd codon position. Correspondence analysis suggested that the pattern of CUB was different among the classes of Arthropoda. Further, it was revealed from the neutrality plot that natural selection had a dominant role while mutation pressure exhibited a minor role in structuring the pattern of codon usage in all the classes of Arthropoda across COI, COII and COIII genes.

Codon usage bias in radioresistant bacteria.

The relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species.