Directional mutation pressure and neutral molecular evolution

Selective and non-selective evolutionary signatures found in the simplest replicative biological entities

Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage.

Differentially used codons among essential genes in bacteria identified by machine learning-based analysis

Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-expression and low-expression genes in several bacteria. In this article, we have extended codon usage study considering gene essentiality as a feature. Using machine learning (ML) based approaches, we have analysed Relative Synonymous Codon Usage (RSCU) values between essential and non-essential genes in Escherichia coli and thirty-four other bacterial genomes whose gene essentiality features were available in public databases. We observed significant differences in codon usage patterns between essential and non-essential genes for majority of the bacterial genomes and accordingly, ML based classifiers achieved high area under curve (AUC) scores, with a minimum score of 70.0 across twenty-eight organisms. Further, importance of the codons towards classifying genes found to differ among the codons in each genome. Arg codon CGT and Gly codon GGT were observed to be the most preferred codons among essential genes in Escherichia coli. Interestingly, some of the codons like CGT, ATA, GGT and GGG observed to be contributing consistently towards classifying essential genes across thirty-five bacteria genomes studied. In other hand, codons TGY and CAY encoding amino acids Cys and His respectively were among the least contributing codons towards classification among all these bacteria. This study demonstrates the gene essentiality based differences in synonymous codon usage in bacteria genomes and presents a common codon usage pattern across bacteria.

The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea

We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome  and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.

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.

Comparative Analysis of the Mitochondrial Genomes of Three Species of Yangiella (Hemiptera: Aradidae) and the Phylogenetic Implications of Aradidae

The mitochondrial genomes of three species of Yangiella were sequenced, annotated, and analyzed. The genome length of the three species of the genus is 15,070-15,202 bp, with a typical gene number, including a control region, 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 13 protein-coding genes (PCGs). It was found that the mitochondrial genome of Yangiella had AT bias. Except for the lack of a DHU arm of the trnS1 gene, the other tRNAs had a typical cloverleaf structure, and the codon usage preferences of the three species exhibited high similarity. In addition, tRNA gene rearrangements were observed among the three subfamilies of Aradidae (Mezirinae, Calisiinae, Aradinae), and it was found that codon usage preferences appeared to be less affected by base mutation and more by natural selection. The Pi and Ka/Ks values indicated that cox1 was the most conserved gene in the mitochondrial genome of Aradidae, while atp8 and nad6 were rapidly evolved genes. Substitution saturation level analysis showed that the nucleic acid sequence of mitochondrial protein-coding genes in Aradidae did not reach saturation, suggesting the rationality of the phylogenetic analysis data. Bayesian and maximum likelihood methods were used to analyze the phylogeny of 16 species of Hemiptera insects, which supported the monophyly of Aneurinae, Carventinae, and Mezirinae, as well as the monophyly of Yangiella. Based on fossils and previous studies, the differentiation time was inferred, indicating that Yangiella diverged about 57 million years ago.

Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns

The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities and determinants of gene evolution in primitive plant species, and identify appropriate exogenous gene expression platforms, the whole-genome sequences of four distinct species were retrieved from the NCBI database. The findings indicated that Ceratopteris richardii, Adiantum capillus-veneris, and Selaginella moellendorffii exhibited an elevated A/U content in their codon base composition and a tendency to end with A/U. Additionally, S. capillus-veneris had more C/G in its codons and a tendency to end with C/G. The ENC values derived from both ENC-plot and ENC-ratio analyses deviated significantly from the standard curves, suggesting that the codon usage preferences of these four species were primarily influenced by genetic mutations and natural selection, with natural selection exerting a more prominent influence. This finding was further supported by PR2-Plot, neutrality plot analysis, and COA. A combination of RSCU and ENC values was used as a reference criterion to rank the codons and further identify the optimal codons. The study identified 24 high-frequency codons in C. richardii, A. capillus-veneris, and Diphasiastrum complanatum, with no shared optimal codons among the four species. Arabidopsis thaliana and Ginkgo biloba exhibited similar codon preferences to the three species, except for S. moellendorffii. This research offers a theoretical framework at the genomic codon level for investigating the phylogenetic relationships between lycophytes and ferns, shedding light on gene codon optimization and its implications for genetic engineering in breeding.

JW, Vieira DBR, Brandão RCF, Medeiros DBDA, Nunes Neto JP. Sequencing and Description of the Mitochondrial Genome of Orthopodomyia fascipes (Diptera: Culicidae)

The genus Orthopodomyia Theobald, 1904 (Diptera: Culicidae) comprises 36 wild mosquito species, with distribution largely restricted to tropical and temperate areas, most of which are not recognized as vectors of epidemiological importance due to the lack of information related to their bionomy and involvement in the cycle transmission of infectious agents. Furthermore, their evolutionary relationships are not completely understood, reflecting the scarcity of genetic information about the genus. Therefore, in this study, we report the first complete description of the mitochondrial genome of a Neotropical species representing the genus, Orthopodomyia fascipes Coquillet, 1906, collected in the Brazilian Amazon region. Using High Throughput Sequencing, we obtained a mitochondrial sequence of 15,598 bp, with an average coverage of 418.5×, comprising 37 functional subunits and a final portion rich in A + T, corresponding to the control region. The phylogenetic analysis, using Maximum Likelihood and Bayesian Inference based on the 13 protein-coding genes, corroborated the monophyly of Culicidae and its two subfamilies, supporting the proximity between the tribes Orthopodomyiini and Mansoniini, partially disagreeing with previous studies based on the use of molecular and morphological markers. The information generated in this study contributes to a better understanding of the taxonomy and evolutionary history of the genus and other groups of Culicidae.

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.

Analysis of codon usage bias of exonuclease genes in invertebrate iridescent viruses

Invertebrate iridescent viruses (IIVs) are double-stranded DNA viruses that belong to the Iridoviridae family. IIVs result diseases that vary in severity from subclinical to lethal in invertebrate hosts. Codon usage bias (CUB) analysis is a versatile method for comprehending the genetic and evolutionary aspects of species. In this study, we analyzed the CUB in 10 invertebrate iridescent viruses exonuclease genes by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results revealed that IIVs exonuclease genes are rich in A/T. The ENC analysis displayed a low codon usage bias in IIVs exonuclease genes. ENC-plot, neutrality plot, and parity rule 2 plot demonstrated that besides mutational pressure, other factors like natural selection, dinucleotide content, and aromaticity also contributed to CUB. The findings could enhance our understanding of the evolution of IIVs exonuclease genes.

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.

Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity

Neboviruses (NeVs) from the Caliciviridae family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.

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.

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.

Relative synonymous codon usage and codon pair analysis of depression associated genes

Depression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to decreased quality of life. We examined 18 genes available at the genetic testing registry (GTR) from the National Center for Biotechnological Information to investigate molecular patterns present in depression-associated genes. Different genotypes and differential expression of the genes are responsible for ensuing depression. The present study, investigated codon pattern analysis, which might play imperative roles in modulating gene expression of depression-associated genes. Of the 18 genes, seven and two genes tended to up- and down-regulate, respectively, and, for the remaining genes, different genotypes, an outcome of SNPs were responsible alone or in combination with differential expression for different conditions associated with depression. Codon context analysis revealed the abundance of identical GTG-GTG and CTG-CTG pairs, and the rarity of methionine-initiated codon pairs. Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. Other molecular signatures also revealed the role of evolutionary forces in shaping codon usage.

Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid?

Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?

Evolutionary analysis and biological characterization of a novel alphabaculovirus isolated from Mythimna separata

Baculoviruses are insect-specific pathogens. Novel baculovirus isolates provide new options for the biological control of pests. Therefore, research into the biological characteristics of newly isolated baculoviruses, including accurate classification and nomenclature, is important. In this study, a baculovirus was isolated from Mythimna separata and its complete genome sequence was determined by next-generation sequencing. The double-stranded DNA genome was 153 882 bp in length, encoding 163 open reading frames. The virus was identified as a variant of Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) and designated Mamestra brassicae multiple nucleopolyhedrovirus CHN1 (MbMNPV-CHN1) according to ultrastructural analysis, genome comparison and phylogenetic analysis. Phylogenetic inference placed MbMNPV-CHN1 in a clade containing isolates of MacoNPV-A, MacoNPV-B and MbMNPV, which we have designated the Mb-McNPV group. The genomes of isolates in the Mb-McNPV group exhibited a high degree of collinearity with relatively minor differences in the content of annotated open reading frames. The development of codon usage bias in the Mb-McNPV group was affected mainly by natural selection. MbMNPV-CHN1 shows high infectivity against seven species of Lepidoptera. The yield of MbMNPV-CHN1 in the fourth- and fifth-instar M. separata larvae was 6.25×109-1.23×1010 OBs/cadaver. Our data provide insights into the classification, host range and virulence differences among baculoviruses of the Mb-McNPV group, as well as a promising potential new baculoviral insecticide.

Assembly and comparative analysis of the first complete mitochondrial genome of a traditional Chinese medicine Angelica biserrata (Shan et Yuan) Yuan et Shan

Duhuo, a member of the Angelica family, is widely used to treat ailments such as rheumatic pain. It possesses a diverse array of bioactivities, including anti-tumor, anti-inflammatory, and analgesic properties, as recent pharmacological research has revealed. Nevertheless, the mtDNA of Angelica species remains relatively unexplored. To address this gap, we sequenced and assembled the mtDNA of A. biserrata to shed light on its genetic mechanisms and evolutionary pathways. Our investigation indicated a distinctive multi-branched conformation in the A. biserrata mtDNA. A comprehensive analysis of protein-coding sequences (PCGs) across six closely related species revealed the presence of 11 shared genes in their mitochondrial genomes. Intriguingly, positive selection emerged as a significant factor in the evolution of the atp4, matR, nad3, and nad7 genes. In addition, our data highlighted a recurring trend of homologous fragment migration between chloroplast and mitochondrial organelles. We identified 13 homologous fragments spanning both chloroplast and mitochondrial genomes. The phylogenetic tree established a close relationship between A. biserrata and Saposhnikovia divaricata. To sum up, our research would contribute to the application of population genetics and evolutionary studies in the genus Acanthopanax and other genera in the Araliaceae family.

Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina

BACKGROUND

Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina.

RESULTS

Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina. The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships.

CONCLUSIONS

There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina.

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.

Genome evolution of Buchnera aphidicola (Gammaproteobacteria): Insights into strand compositional asymmetry, codon usage bias, and phylogenetic implications

Taxa of Buchnera aphidicola (hereafter "Buchnera") are mutualistic intracellular symbionts of aphids, known for their remarkable biological traits such as genome reduction, strand compositional asymmetry, and symbiont-host coevolution. With the growing availability of genomic data, we performed a comprehensive analysis of 103 genomes of Buchnera strains from 12 host subfamilies, focusing on the genomic characterizations, codon usage patterns, and phylogenetic implications. Our findings revealed consistent features among all genomes, including small genome sizes, low GC contents, and gene losses. We also identified strong strand compositional asymmetries in all strains at the genome level. Further investigation suggested that mutation pressure may have played a crucial role in shaping codon usage of Buchnera. Moreover, the genomic asymmetries were reflected in asymmetric codon usage preferences within chromosomal genes. Notably, the levels of these asymmetries were varied among strains and were significantly influenced by the degrees of genome shrinkages. Lastly, our phylogenetic analyses presented an alternative topology of Aphididae, based on the Buchnera symbionts, providing robust confirmation of the paraphylies of Eriosomatinae, and Macrosiphini. Our objectives are to further understand the strand compositional asymmetry and codon usage bias of Buchnera taxa, and provide new perspectives for phylogenetic studies of Aphididae.

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.

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.

Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation

Goose astroviruses (GoAstVs) are causative agents that account for fatal infection of goslings characterized by visceral urate deposition, resulting in severe economic losses in major goose-producing regions in China since 2017. In this study, we sought to unravel the intrinsic properties associated with adaptation and evolution in the host environment of GoAstVs. Consistent results from phylogenetic analysis and correspondence analysis performed on the codon usage patterns (CUPs) reveal 2 clusters of GoAstVs, namely, GoAstV-1 and GoAstV-2. However, multiple similar compositional characteristics were found, despite the high divergence between GoAstV-1 and GoAstV-2. Studies on the base composition of GoAstVs reveal an A/U bias, indicating a compositional constraint, while natural selection prevailed in determining the CUPs in the virus genome based on our neutrality plot analysis, reflecting high adaptive pressure to fit the host environment. Codon adaptation index (CAI) analysis revealed a higher degree of fitness to the CUPs of the corresponding host for GoAstVs than avian influenza virus and betacoronaviruses, which may be a favorable factor contributing to the high pathogenicity and wide distribution of GoAstVs in goslings. In addition, GoAstVs were less adapted to ducks and chickens, with significantly lower CAI values than to geese, which may be a reason for the different prevalence of GoAstVs among these species. Extensive investigations on dinucleotide distribution revealed a significant suppression of the CpG and UpA motifs in the virus genome, which may facilitate adaptation to the host's innate immune system by evading surveillance. In addition, our study reported the trends of increasing fitness to the host's microenvironment for GoAstVs through increasing adaptation to host CUPs and ongoing reduction of CpG motifs in the virus genome. The present analysis deepens our understanding of the basic biology, pathogenesis, adaptation and evolutionary pattern of GoAstVs, and contributes to the development of novel antiviral strategies.

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.

The parapoxvirus Orf virus inhibits dsDNA-mediated type I IFN expression via STING-dependent and STING-independent signalling pathways

Type I interferons (IFNs) are critical in the host defence against viruses. They induce hundreds of interferon-stimulated genes (ISGs) many of which have an antiviral role. Poxviruses induce IFNs via their pathogen-associated molecular patterns, in particular, their genomic DNA. In a majority of cell types, dsDNA is detected by a range of cytoplasmic DNA sensors that mediate type I IFN expression via stimulator of interferon genes (STING). Orf virus (ORFV) induces cutaneous pustular skin lesions and is the type species of the Parapoxvirus genus within the Poxviridae family. The aim of this study was to investigate whether ORFV modulates dsDNA-induced type I IFN expression via STING-dependent signalling pathways in human dermal fibroblasts (hNDF) and THP-1 cells. We showed that ORFV infection of these cell types treated with poly(dA:dT) resulted in strong inhibition of expression of IFN-β. In hNDFs, we showed using siRNA knock-down that STING was essential for type I IFN induction. IFN-β expression was further reduced when both STING and RIG-I were knocked down. In addition, HEK293 cells that do not express STING or Toll-like receptors also produce IFN-β following stimulation with poly(dA:dT). The 5' triphosphate dsRNA produced by RNA polymerase III specifically results in the induction of type I IFNs through the RIG-I receptor. We showed that ORFV infection resulted in strong inhibition of IFN-β expression in HEK293 cells stimulated with poly(dA:dT). Overall, this study shows that ORFV potently counteracts the STING-dependent and STING-independent IFN response by antagonizing dsDNA-activated IFN signalling pathways.

Mutation and codon bias analysis of the spike protein of Omicron, the recent variant of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is a heavily mutated virus and designated as a variant of concern. To investigate the codon usage pattern of this new variant, we performed mutation and codon bias analysis for Omicron as well as for its sub-lineages BA.1 and BA.2 and compared them with the original SARS-CoV-2 and the Delta variant sequences obtained in this study. Our results indicate that the sub-lineage BA.1 and BA.2 have up to 23 sites of difference on the spike protein, which have minimal impact on function. The Omicron variant and its sub-lineages have similar codon usage patterns and A/U ending codons appear to be preferred over G/C ending codons. The Omicron has a lower degree of codon usage bias in spite of evidence that natural selection, mutation pressure and dinucleotide abundance shape the codon usage bias of Omicron, with natural selection being more significant on BA.2 than the other sub-lineages of Omicron. The codon usage pattern of Omicron variant that we explored provides valid information for a clearer understanding of Omicron and its sub-lineages, which could find application in vaccine development and optimization.

Analysis of codon usage patterns of porcine enteric alphacoronavirus and its host adaptability

Porcine enteric alphacoronavirus (PEAV) is a newly emerging swine enteropathogen that poses a threat to the swine industry. To understand the PEAV genome evolution, we performed a comprehensive analysis of the codon usage patterns in fifty-nine PEAV strains currently available. Phylogenetic analysis showed that PEAV can be divided into six lineages. Effective number of codons analysis demonstrated that the PEAV genome exhibits a low codon usage bias (CUB). Nucleotide composition analysis indicated that the PEAV genome has the most abundant nucleotide U content, with GC content (39.37% ± 0.08%) much lower than AU content (60.63% ± 0.08%). Neutrality and effective number of codons plot analyses suggested that natural selection rather than mutation pressure dominates the CUB of PEAV. Host adaptation analysis revealed that PEAV fits the codon usage pattern of non-human primates, humans and mice better than that of pigs. Our data enriches information on PEAV evolution, host adaptability, and cross-species transmission.

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.

Forecasting influenza hemagglutinin mutations through the lens of anomaly detection

The influenza virus hemagglutinin is an important part of the virus attachment to the host cells. The hemagglutinin proteins are one of the genetic regions of the virus with a high potential for mutations. Due to the importance of predicting mutations in producing effective and low-cost vaccines, solutions that attempt to approach this problem have recently gained significant attention. A historical record of mutations has been used to train predictive models in such solutions. However, the imbalance between mutations and preserved proteins is a big challenge for the development of such models that need to be addressed. Here, we propose to tackle this challenge through anomaly detection (AD). AD is a well-established field in Machine Learning (ML) that tries to distinguish unseen anomalies from normal patterns using only normal training samples. By considering mutations as anomalous behavior, we could benefit existing rich solutions in this field that have emerged recently. Such methods also fit the problem setup of extreme imbalance between the number of unmutated vs. mutated training samples. Motivated by this formulation, our method tries to find a compact representation for unmutated samples while forcing anomalies to be separated from the normal ones. This helps the model to learn a shared unique representation between normal training samples as much as possible, which improves the discernibility and detectability of mutated samples from the unmutated ones at the test time. We conduct a large number of experiments on four publicly available datasets, consisting of three different hemagglutinin protein datasets, and one SARS-CoV-2 dataset, and show the effectiveness of our method through different standard criteria.

Codon usage pattern of the ancestor of green plants revealed through Rhodophyta

Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.

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.

Distinguishing Genetic Drift from Selection in Papillomavirus Evolution

Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.

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.

Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak

The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the monkeypox virus (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution.

Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities

Introduction

Neurodegeneration and cancer present in comorbidities with inverse effects due to the expression of genes and pathways acting in opposition. Identifying and studying the genes simultaneously up or downregulated during morbidities helps curb both ailments together.

Methods

This study examines four genes. Three of these (Amyloid Beta Precursor Protein (APP), Cyclin D1 (CCND1), and Cyclin E2 (CCNE2) are upregulated, and one protein phosphatase 2 phosphatase activator (PTPA) is simultaneously downregulated in both disorders. We investigated molecular patterns, codon usage, codon usage bias, nucleotide bias in the third codon position, preferred codons, preferred codon pairs, rare codons, and codon context.

Results

Parity analysis revealed that T is preferred over A, and G is preferred over C in the third codon position, suggesting composition plays no role in nucleotide bias in both the upregulated and downregulated gene sets and that mutational forces are stronger in upregulated gene sets than in downregulated ones. Transcript length influenced the overall %A composition and codon bias, and the codon AGG exerted the strongest influence on codon usage in both the upregulated and downregulated gene sets. Codons ending in G/C were preferred for 16 amino acids, and glutamic acid-, aspartic acid-, leucine-, valine-, and phenylalanine-initiated codon pairs were preferred in all genes. Codons CTA (Leu), GTA (Val), CAA (Gln), and CGT (Arg) were underrepresented in all examined genes.

Discussion

Using advanced gene editing tools such as CRISPR/Cas or any other gene augmentation technique, these recoded genes may be introduced into the human body to optimize gene expression levels to augment neurodegeneration and cancer therapeutic regimens simultaneously.

Comparative Mitogenomics of Jumping Spiders with First Complete Mitochondrial Genomes of Euophryini (Araneae: Salticidae)

Salticidae is the most species-rich family of spiders with diverse morphology, ecology and behavior. However, the characteristics of the mitogenomes within this group are poorly understood with relatively few well-characterized complete mitochondrial genomes. In this study, we provide completely annotated mitogenomes for Corythalia opima and Parabathippus shelfordi, which represent the first complete mitogenomes of the tribe Euophryini of Salticidae. The features and characteristics of the mitochondrial genomes are elucidated for Salticidae by thoroughly comparing the known well-characterized mitogenomes. The gene rearrangement between trnL2 and trnN was found in two jumping spider species, Corythalia opima and Heliophanus lineiventris Simon, 1868. Additionally, the rearrangement of nad1 to between trnE and trnF found in Asemonea sichuanensis Song & Chai, 1992 is the first protein-coding gene rearrangement in Salticidae, which may have an important phylogenetic implication for the family. Tandem repeats of various copy numbers and lengths were discovered in three jumping spider species. The codon usage analyses showed that the evolution of codon usage bias in salticid mitogenomes was affected by both selection and mutational pressure, but selection may have played a more important role. The phylogenetic analyses provided insight into the taxonomy of Colopsus longipalpis (Żabka, 1985). The data presented in this study will improve our understanding of the evolution of mitochondrial genomes within Salticidae.

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.

Compositional biases and evolution of the largest plant RNA virus order Patatavirales

Patatavirales is the largest order of plant RNA viruses and exclusively contains the family Potyviridae, accounting for 30 % of all known plant viruses. The composition bias of animal RNA viruses and several plant RNA viruses has been determined. However, the comprehensive nucleic acid composition, codon pair usage patterns, dinucleotide preference and codon pair preference of plant RNA viruses have not been investigated to date. In this study, integrated analysis and discussion of the nucleic acid composition, codon usage patterns, dinucleotide composition and codon pair bias of potyvirids were performed using 3732 complete genome coding sequences. The nucleic acid composition of potyvirids was significantly enriched in A/U. Interestingly, the A/U-rich nucleotide composition of Patatavirales is essential for determining the preferred A-ended and U-ended codons and the overexpression of UpG and CpA dinucleotides. The codon usage patterns and codon pair bias of potyvirids were significantly correlated with their nucleic acid composition. Additionally, the codon usage pattern, dinucleotide composition and codon-pair bias of potyvirids are more dependent on the classification of the virus compared with their hosts. Our analysis provides a better understanding of future research on the origin and evolution patterns of the order Patatavirales.

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Saxifragales is a 15-family order of early-divergent Eudicots with a rich morphological diversity and an ancient rapid radiation. Codon usage bias (CUB) analyses have emerged as an essential tool for understanding the evolutionary dynamics in genes. Thus far, the codon utilization patterns had only been reported in four separate genera within Saxifragales. This study provides a comprehensive assessment of the codon manipulation based on 50 plastid genes, covering 11 constituent families at a larger sampling scale. Our results first showed a high preference for AT bases and AT-ending codons. We then used effective number of codons (ENC) to assess a range of codon bias levels in the plastid genes. We also detected high-informative intrafamilial differences of ENC in three families. Subsequently, parity rule 2 (PR2) plot analyses revealed both family-unique and order-shared bias patterns. Most importantly, the ENC plots and neutrality analyses collectively supported the dominant roles of selection in the CUB of Saxifragales plastid genes. Notably, the phylogenetic affinities inferred by both ML and BI methods were consistent with each other, and they all comprised two primary clades and four subclades. These findings significantly enhance our understanding of the evolutionary processes of the Saxifrage order, and could potentially inspire more CUB analyses at higher taxonomic levels.

Non-random Codon Usage of Synonymous and Non-synonymous Mutations in the Human HLA-A Gene

The structure and function of human leucocyte antigen (HLA-A) is well known and is an extremely variable protein. From the public HLA-A database, we chose 26 high frequency HLA-A alleles (45% of sequenced alleles). Using five arbitrary references from these alleles, we analyzed synonymous mutations at the third codon position (sSNP₃) and non-synonymous mutations (NSM). Both mutation types showed non-random locations of 29 sSNP₃ codons and 71 NSM codons in the five reference lists. Most sSNP₃ codons show identical mutation types with many mutations resulting from cytosine deamination. We proposed 23 ancestral parents of sSNP₃ in five reference sequences using conserved parents in five unidirectional codons and 18 majority parents in reciprocal codons. These 23 proposed ancestral parents show exclusive codon usage of G₃ or C₃ parents located on both DNA strands that mutate to A₃ or T₃ variants mostly (76%) by cytosine deamination The sSNP₃ and NSM show clear separation of the two variant types with most sSNP₃ located in conserved areas in exons 2, 3 and 4, compared to most NSM appearing in two Variable Areas with no sSNP₃ in the latter parts of exons 2 (α1) and 3 (α2). The Variable Areas contain NSM (polymorphic) residues at the center of the groove that bind the foreign peptide. We find distinctly different mutation patterns in NSM codons from those of sSNP₃. Namely, G-C to A-T mutation frequency was much smaller, suggesting that evolutional pressures of deamination and other mechanisms applied to the two areas are significantly different.

Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)

Codon usage bias (CUB) reveals the characteristics of species and can be utilized to understand their evolutionary relationship, increase the target genes' expression in the heterologous receptor plants, and further provide theoretic assistance for correlative study on molecular biology and genetic breeding. The chief aim of this work was to analyze the CUB in chloroplast (cp.) genes in nine Elaeagnus species to provide references for subsequent studies. The codons of Elaeagnus cp. genes preferred to end with A/T bases rather than with G/C bases. Most of the cp. genes were prone to mutation, while the rps7 genes were identical in sequences. Natural selection was inferred to have a powerful impact on the CUB in Elaeagnus cp. genomes, and their CUB was extremely strong. In addition, the optimal codons were identified in the nine cp. genomes based on the relative synonymous codon usage (RSCU) values, and the optimal codon numbers were between 15 and 19. The clustering analyses based on RSCU were contrasted with the maximum likelihood (ML)-based phylogenetic tree derived from coding sequences, suggesting that the t-distributed Stochastic Neighbor Embedding clustering method was more appropriate for evolutionary relationship analysis than the complete linkage method. Moreover, the ML-based phylogenetic tree based on the conservative matK genes and the whole cp. genomes had visible differences, indicating that the sequences of specific cp. genes were profoundly affected by their surroundings. Following the clustering analysis, Arabidopsis thaliana was considered the optimal heterologous expression receptor plant for the Elaeagnus cp. genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01289-6.

Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

BACKGROUND

Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported.

RESULTS

In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates.

CONCLUSIONS

The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.

A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations

The Usutu virus (USUV) is an emerging arbovirus virus maintained in the environment of Afro-Eurasia via a bird-mosquito-bird enzootic cycle and sporadically infected other vertebrates. Despite primarily asymptomatic or mild symptoms, humans infected by USUV can develop severe neurological diseases such as meningoencephalitis. However, no detailed study has yet been conducted to investigate its evolution from the perspective of codon usage patterns. Codon usage choice of viruses reflects the genetic variations that enable them to reconcile their viability and fitness toward the external environment and new hosts. This study performed a comprehensive evolution and codon usage analysis of USUVs. Our reconstructed phylogenetic tree confirmed that the circulation viruses belong to eight distinct lineages, reaffirmed by principal component analysis based on codon usage patterns. We also found a relatively small codon usage bias and that natural selection, mutation pressure, dinucleotide abundance, and evolutionary processes collectively shaped the codon usage of the USUV, with natural selection predominating over the others. Additionally, a complex interaction of codon usage between the USUV and its host was observed. This process could have enabled USUV to adapt to various hosts and vectors, including humans. Therefore, the USUV may possess a potential risk of cross-species transmission and subsequent outbreaks. In this respect, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.

Evolution of codon usage in Taenia saginata genomes and its impact on the host

The beef tapeworm, also known as Taenia saginata, is a zoonotic tapeworm from the genus Taenia in the order Cyclophyllidea. Taenia saginata is a food-borne zoonotic parasite with a worldwide distribution. It poses serious health risks to the host and has a considerable negative socioeconomic impact. Previous studies have explained the population structure of T. saginata within the evolutionary time scale and adaptive evolution. However, it is still unknown how synonymous codons are used by T. saginata. In this study, we used 90 T. saginata strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in the genome of T. saginata. Further low CUB was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection was involved in the structuring of CUB in T. saginata. Further analysis showed that T. saginata has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Generally, both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in T. saginata. This study is important because it characterized the codon usage pattern in the T. saginata genomes and provided the necessary data for a basic evolutionary study on them.

Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species

BACKGROUND

The Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by environmental factors, base mutation, gene flow and gene expression level, among which natural selection and mutation pressure are the main factors. The study of codon preference is an effective method to analyze the source of evolutionary driving forces in organisms. Epimedium species are perennial herbs with ornamental and medicinal value distributed worldwide. The chloroplast genome is self-replicating and maternally inherited which is usually used to study species evolution, gene expression and genetic transformation.

RESULTS

The results suggested that chloroplast genomes of Epimedium species preferred to use codons ending with A/U. 17 common high-frequency codons and 2-6 optimal codons were found in the chloroplast genomes of Epimedium species, respectively. According to the ENc-plot, PR2-plot and neutrality-plot, the formation of codon preference in Epimedium was affected by multiple factors, and natural selection was the dominant factor. By comparing the codon usage frequency with 4 common model organisms, it was found that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae were suitable exogenous expression receptors.

CONCLUSION

The evolutionary driving force in the chloroplast genomes of 10 Epimedium species probably comes from mutation pressure. Our results provide an important theoretical basis for evolutionary analysis and transgenic research of chloroplast genes.

The effect of the genomic GC content bias of prokaryotic organisms on the secondary structures of their proteins

One of the main characteristics of prokaryotic genomes is the ratio in which guanine-cytosine bases are used in their DNA sequences. This is known as the genomic GC content and varies widely, from values below 20% to values greater than 74%. It has been demonstrated that the genomic GC content varies in accordance with the phylogenetic distribution of organisms and influences the amino acid composition of their corresponding proteomes. This bias is particularly important for amino acids that are coded by GC content-rich codons such as alanine, glycine, and proline, as well as amino acids that are coded by AT-rich codons, such as lysine, asparagine, and isoleucine. In our study, we extend these results by considering the effect of the genomic GC content on the secondary structure of proteins. On a set of 192 representative prokaryotic genomes and proteome sequences, we identified through a bioinformatic study that the composition of the secondary structures of the proteomes varies in relation to the genomic GC content; random coils increase as the genomic GC content increases, while alpha-helices and beta-sheets present an inverse relationship. In addition, we found that the tendency of an amino acid to form part of a secondary structure of proteins is not ubiquitous, as previously expected, but varies according to the genomic GC content. Finally, we discovered that for some specific groups of orthologous proteins, the GC content of genes biases the composition of secondary structures of the proteins for which they code.

Characterization of mitochondrial genome of Indian Ocean blue-spotted maskray, Neotrygon indica and its phylogenetic relationship within Dasyatidae Family

The present study characterized complete mitochondrial genome of Blue-spotted maskray, Neotrygon indica and studied the evolutionary relationship of the species within the Dasyatidae family. The total length of the mitogenome was 17,974 bp including 37 genes and a non-coding control region. The average frequency of nucleotides in protein-coding genes was A: 29.1 %, T: 30.2 %, G: 13.0 % and C: 27.7 % with AT content of 59.3 %. The values of AT and GC skewness were -0.018 and -0.338, respectively. Comparative analyses showed a large number of average synonymous substitutions per synonymous site (Ks) in gene NADH4 (5.07) followed by NADH5 (4.72). High values of average number of non-synonymous substitutions per non-synonymous site (Ka) were observed in genes ATPase8 (0.54) and NADH2 (0.44). Genes NADH4L and NADH2 showed high interspecific genetic distance values of 0.224 ± 0.001 and 0.213 ± 0.002, respectively. Heat map analysis showed variation in codon usage among different species of the Dasyatidae family. The phylogenetic tree showed a sister relationship between the Dasyatinae and the Neotrygoninae subfamilies. Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. Based on the present results, Neotrygon indica could have diverged from the common ancestor of the two latter in the Plio-Pleistocene. The present study showed distinct characteristics of N. indica from its congeners through comparative mitogenomics.