Low Codon Usage Bias Research Articles

Codon Usage Analysis Reveals Distinct Evolutionary Patterns and Host Adaptation Strategies in Duck Hepatitis Virus 1 (DHV-1) Phylogroups.

Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.

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

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

Comparative analysis of codon usage patterns of venom gland-specific honeybee-infecting viruses in solitary hunting and social wasps

To identify the evolutionary traits of honeybee-infecting viruses (HVs), including black queen cell virus (BQCV), deformed wing virus (DWV), and Israeli acute paralysis virus (IAPV), and their adaptation patterns in the venom gland of different hosts, we conducted a comparative analysis of codon usage patterns of venom gland-specific HVs in honeybees, solitary hunting, and social wasps. The nucleotides A and U, as well as the nucleotide composition at the third position of synonymous codons (A3s and U3s), were abundantly present with high frequencies in the polyprotein region of the three HVs in Apis mellifera, solitary hunting, and social wasps. Although the three HVs exhibited a high codon adaptation index, effective number of codons and the frequencies of GC3s were observed to be high and low, respectively, indicating a low codon usage bias in the three HVs. The relative abundance of dinucleotides, nucleotide compositions, and the aromaticity of amino acids might be considered as reasons for the different codon usage patterns of the three HVs in solitary hunting and social wasps compared to A. mellifera. The result of phylogenetic analysis revealed that DWV possesses a unique evolutionary pattern compared to the lineages of Aculeate species, possibly caused by specific ecological interactions. Our study provides further insights into the evolutionary aspects of venom gland-specific HVs in Aculeate species and might contribute as fundamental information for further research on the evolution of HVs.

A Comprehensive Comparative Analysis on the Codon Usage Bias of DNA Polymerase Genes in Invertebrate Iridescent Viruses

Invertebrate iridescent viruses (IIVs) are classified as double-stranded DNA viruses within the Iridoviridae family. IIVs are viruses that infect invertebrate hosts, causing symptoms that vary in intensity from slight reductions in host fitness to systemic disease. Numerous earlier investigations have provided insights into the genomic, proteomic, and transcriptional analyses of invertebrate iridescent viruses. However, the codon usage bias (CUB) of IIVs has yet to be fully understood. In order to gain a more profound insight into the evolutionary features of IIVs, we conducted an extensive analysis of the codon usage patterns in the DNA polymerase genes (DNA pol genes) of 12 invertebrate iridescent viruses. The analysis of both nucleotide composition and relative synonymous codon usage (RSCU) indicated a higher prevalence of AT-ended codons in the DNA pol genes of IIVs. Additionally, a low codon usage bias was determined from the effective number of codons (ENC) value. Analyses of ENC-GC3s plot, neutrality plot, and parity rule 2 plot illustrated that the codon usage patterns in IIVs DNA pol genes were influenced by both natural selection and mutational pressure. This investigation holds significance as it has delineated the codon usage patterns within the DNA pol genes of IIVs and has furnished crucial data for a foundational study of their evolutionary aspects.

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.

A detailed analysis of codon usages bias and influencing factors in the nucleocapsid gene of Nipah Virus

Several outbreaks of Nipah Virus (NiV) have recently been reported in various parts of the world including India. The 18.2-kb size single-stranded negative-sense RNA genome of NiV has six genes that encode nine proteins. Among nine, the nucleoprotein (N) protein is the most abundant viral protein. The relative availability of N protein is a determining factor for the activation of genome encapsidation, replicase activity, and regulating viral RNA synthesis. In this study, we have conducted a codon usage analysis of N protein-encoding gene (N gene) of NiV. The relative synonymous codon usage (RSCU) values, in combination with an ENC value of 51.048, represented low codon usage bias in the N gene. The effect of mutational pressure on codon usage bias was confirmed by significant correlations of GC3s, G3s, C3s, A3s, U3s, and ENC values with whole nucleotide contents (GC%, G%, C%, A%, and U%). Correlation study of GC3s, G3s, C3s, A3s, and U3s with axis values of correspondence analysis (CA) also supported the role of mutational pressure. The correlation study of Gravy values with GC3s, G3s, C3s, A3s, and U3s revealed the presence of natural selection in addition to mutational pressure on codon usage bias. Moreover, NiV codon adaptation index (CAI) value higher than their corresponding expected CAI (eCAI) values against human (CAI, 0.726; eCAI, 0.715), pig (CAI, 0.837; eCAI, 0.819), and bat (CAI, 0.762; eCAI, 0.750) also indicated natural selection play role on codon usage bias. Additionally, geographical distribution, and evolutionary processes also influenced the codon usage bias to some extent.

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.

Synonymous sites for accessibility around microRNA binding sites in bacterial spot and speck disease resistance genes of tomato.

The major causes of mass tomato infections in both covered and open ground are agents of bacterial spot and bacterial speck diseases. MicroRNAs (miRNAs) are 16-21 nucleotides in length, non-coding RNAs that inhibit translation and trigger mRNA degradation. MiRNAs play a significant part in plant resistance to abiotic and biotic stresses by mediating gene regulation via post-transcriptional RNA silencing. In this study, we analyzed a collection of bacterial resistance genes of tomato and their binding sites for tomato miRNAs and Pseudomonas syringe pv. tomato miRNAs. Our study found that two genes, bacterial spot disease resistance gene (Bs4) and bacterial speck disease resistance gene (Prf), have a 7mer-m8 perfect seed match with miRNAs. Bs4 was targeted by one tomato miRNA (sly-miR9470-3p) and three Pseudomonas syringe pv. tomato miRNAs (PSTJ4_3p_27246, PSTJ4_3p_27246, and PSTJ4_3p_27246). Again, Prf gene was found to be targeted by two tomato miRNAs namely, sly-miR9469-5p and sly-miR9474-3p. The accessibility of the miRNA-target site and its flanking regions and the relationship between relative synonymous codon usage and tRNAs were compared. Strong access to miRNA targeting regions and decreased rate of translations suggested that miRNAs might be efficient in binding to their particular targets. We also found the existence of rare codons, which suggests that it could enhance miRNA targeting even more. The codon usage pattern analysis of the two genes revealed that both were AT-rich (Bs4 = 63.2%; Prf = 60.8%). We found a low codon usage bias in both genes, suggesting that selective restriction might regulate them. The silencing property of miRNAs would allow researchers to discover the involvement of plant miRNAs in pathogen invasion. However, the efficient validation of direct targets of miRNAs is an urgent need that might be highly beneficial in enhancing plant resistance to multiple pathogenic diseases.

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.

Multiple genotypes infection and molecular characterization of Torque teno neovison virus: A novel Anelloviridae of mink in China

A novel Torque teno neovison virus (TTVs) was identified in specimens collected from dead mink during an outbreak of the Aleutian mink disease virus. Eighteen complete genomic sequences were obtained, ranging from 2109 to 2158 nucleotides in length and consisting of an untranslated region and three open reading frames. The genomic organization of mink TTVs is similar to previously reported anelloviruses. However, the deduced amino acid sequence of its ORF1 protein shows genetic diversity compared to related anelloviruses, suggesting that it represents a putative new species within the Anelloviridae family. This study provides a detailed molecular characterization of the novel mink anelloviruses, including its codon usage pattern, origin, and evolution. Analysis of the viral genomic sequences reveals the existence of multiple genotypes of co-infection. Principal component analysis and phylogenetic trees confirm the coexistence of multiple genotypes. Furthermore, the codon usage analyses indicate that mink TTVs have a genotype-specific codon usage pattern and show a low codon usage bias. Host-specific adaptation analysis suggests that TTVs are less adapted to mink. The possible origin and evolutionary history of mink TTVs were elucidated. Mink TTVs was genetically closely related to giant panda anellovirus, representing a new species. The observed incongruence between the phylogenetic history of TTVs and that of their hosts suggests that the evolution of anellovirus is largely determined by cross-species transmission. The study provides insights into the co-infection and genetic evolution of anellovirus in China.

Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus

Infectious bronchitis virus (IBV) is distributed worldwide and causes significant losses in the poultry industry. In recent decades, lineages GI-19 and GI-7 have become the most prevalent IBV strains in China. However, the molecular evolution and phylodynamics of the lineage GI-7 IBV strains remain largely unknown. In this study, we identified 19 IBV strains from clinical samples from January 2021 to June 2022 in China, including 12 strains of GI-19, 3 strains of GI-7, and 1 strain each of GI-1, GI-9, GI-13, and GI-28. These results indicated that lineages GI-19 and GI-7 IBVs are still the most prevalent IBVs in China. Here, we investigated the evolution and transmission dynamics of lineage GI-7 IBVs. Our results revealed that the Taiwan province might be the origin of lineage GI-7 IBVs and that South China plays an important role in the spread of IBV. Furthermore, we found low codon usage bias of the S1 gene in lineage GI-7 IBVs. This allowed IBV to replicate in the host during evolution as a result of reduced competition, mainly driven by natural selection and mutational pressure, where the role of natural selection is more prominent. Collectively, our results reveal the genetic diversity and evolutionary dynamics of lineage GI-7 IBVs, which could assist in the prevention and control of viral infection.

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.

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection.

Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.

Codon Pattern and Compositional Constraints Determination of Genes Associated with Chronic Periodontitis.

Genome-wide association studies showed the relationship of NIN, ABHD12B, WHAMM, AP3B2, and SIGLEC5 with chronic periodontitis. The study's objective was to investigate different molecular patterns and evolutionary forces acting on the mentioned genes. The investigation of molecular patterns encompasses the study of compositional parameters, expression profile, physical properties of genes, codon preferences, degree of codon bias, determination of the most influential codons, and assessment of actions of evolutionary forces, such as mutations and natural selection. The overall compositional analysis revealed the dominance of A and G nucleotides compared to T and C. A relatively low codon usage bias is observed. The CTG codon is the most overused codon, followed by TCC. The genes, AP3B2 and SIGLEC5, preferred GC-ending codons, while NIN, ABHD12B, and WHAMM preferred AT-ending codons. The presence of directional mutational force and natural selection was found to operate codon usage in genes envisaged, and selective forces were dominant over mutational forces. Apart from mutation and selection forces, compositional constraints also played imperative roles. The study enriched our knowledge of specific molecular patterns associated with the set of genes significantly associated with chronic periodontitis. Further studies are warranted to identify more genetic signatures associated with the disease.

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy.

Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.

Genome dynamics, codon usage patterns and influencing factors in Aeromonas hydrophila phages

In the present study, genome characteristics and codon usage patterns of 44 Aeromonas hydrophila phages were studied. Phage genomes varied from 30.8 to 262.0 kb with mean±SD and median values of 111.3 ± 81.4 kb and 79.4 kb, respectively. Though the great variation in phage GC contents (35.1–62.2%) was observed, GC contents of all phages (except two phages) were significantly less than the GC content (62.4 ± 5.6%) of the host. The effective number of codons (ENC) values of phage genes ranged from 27.7 to 61 with a mean±SD value of 47.4 ± 6.8. Out of a total 5773 phage genes, 207 (3.6%), 3,528 (61.1%) and 2,012 (34.9%) genes had strong (ENC < 35), moderate (35 < ENC < 50) and low (ENC ≥ 50) codon usage bias, respectively. During relative synonymous codon usage (RSCU) analysis, shared usage of preferred codons was also observed between the phages and host. During codon adaptation index (CAI) analysis, 1028 (17.8%) phage genes showed significant adaptation towards the host. Among these genes, 797 (78.0%) genes encoded hypothetical proteins or proteins of unknown function; whereas 118 (12%) genes encoded the phage structural and packaging proteins. Segregation of ENC, RSCU and CAI analysis results based on genome size also indicated that codon usage bias was more prominent in phages with small genomes. Correlation, neutrality and GC3 versus ENC analyzes indicated a more dominant role of natural selection in shaping the codon usage patterns of A. hydrophila phages. The findings of the current study could be useful from evolutionary and host-pathogen interaction perspectives leading to efficient utilization of phages for therapeutic and other applications.

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

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

Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns.

Neurodegenerative disorders cause irreversible damage to the neurons and adversely affect the quality of life. Protein misfolding and their aggregation in specific parts of the brain, mitochondrial dysfunction, calcium load, proteolytic stress, and oxidative stress are among the causes of neurodegenerative disorders. In addition, altered metabolism has been associated with neurodegeneration as evidenced by reductions in glutamine and alanine in transient global amnesia patients, higher homocysteine-cysteine disulfide, and lower methionine decline in serum urea have been observed in Alzheimer’s disease patients. Neurodegeneration thus appears to be a culmination of altered metabolism. The study’s objective is to analyze various attributes like composition, physical properties of the protein, and factors like selectional and mutational forces, influencing codon usage preferences in a panel of genes involved directly or indirectly in metabolism and contributing to neurodegeneration. Various parameters, including gene composition, dinucleotide analysis, Relative synonymous codon usage (RSCU), Codon adaptation index (CAI), neutrality and parity plots, and different protein indices, were computed and analyzed to determine the codon usage pattern and factors affecting it. The correlation of intrinsic protein properties such as the grand average of hydropathicity index (GRAVY), isoelectric point, hydrophobicity, and acidic, basic, and neutral amino acid content has been found to influence codon usage. In genes up to 800 amino acids long, the GC3 content was highly variable, while GC12 content was relatively constant. An optimum CpG content is present in genes to maintain a high expression level as required for genes involved in metabolism. Also observed was a low codon usage bias with a higher protein expression level. Compositional parameters and nucleotides at the second position of codons played essential roles in explaining the extent of bias. Overall analysis indicated that the dominance of selection pressure and compositional constraints and mutational forces shape codon usage.

Codon usage bias analysis of S-locus genes &amp;lt;italic&amp;gt;SRK&amp;lt;/italic&amp;gt;, &amp;lt;italic&amp;gt;SLG&amp;lt;/italic&amp;gt;, and &amp;lt;italic&amp;gt;SP11/SCR&amp;lt;/italic&amp;gt; in &amp;lt;italic&amp;gt;Brassica oleracea&amp;lt;/italic&amp;gt;

<p id="C3">S-locus is the key locus in <italic>Brassica </italic>that controls the recognition and initiation of the self-incompatibility response. To clarify the codon usage characteristics of the S domain of S-locus genes <italic>SRK</italic> and <italic>SLG</italic> as well as of <italic>SP11/SCR</italic> coding sequence in <italic>Brassica oleracea</italic>, the codon usage bias of 41, 36, and 11 alleles of <italic>SRK</italic>, <italic>SLG</italic>, and <italic>SP11/SCR</italic> were analyzed by Codon W, SPSS, Python, and EMBOSS online tools, respectively. Neutrality, ENC-GC3, and Parity Rule 2 (PR2) plotting together with multivariate statistical analysis were also used for the exploration of possible factors that might affect the formation of the codon usage bias of these genes. The cluster analysis performed using various methods showed that S domains of <italic>SRK</italic>, <italic>SLG</italic>, and <italic>SP11/SCR</italic> genes of <italic>Brassica oleracea</italic> were rich in AT base pairs, the codon preference ended with A/T base and had a lower codon usage bias, which were affected by the natural selection (a main factor) and the mutational pressure (a secondary factor) as well as dinucleotide abundance. Based on the RSCU values, 4 over-expressed codons of <italic>SRK</italic> and <italic>SLG</italic>, and 11 over-expressed codons of <italic>SP11/SCR</italic> were identified. Cluster analysis based on RSCU could accurately reflect the relationship among <italic>SRK</italic>, <italic>SLG</italic>, and <italic>SP11/SCR</italic> alleles in <italic>Brassica oleracea</italic>, which was consistent and reliable with CDS sequence clustering. According to codon usage bias and cluster relationship, the S domain of <italic>SRK</italic> and the <italic>SP11/SCR</italic> coding sequence might be coevolutionary in the codon usage bias. This study enhances our understanding of the mechanism of distribution of codons and the evolution of <italic>SRK</italic>, <italic>SLG</italic>, and <italic>SP11/SCR</italic> genes in <italic>Brasscia oleracea</italic>.

Meta-transcriptomic analysis reveals an isolate of aphid lethal paralysis virus from Wisteria sinensis in Iran

Viral metagenomic analysis of wisteria leaf sample in Iran detected one dicistrovirus: aphid lethal paralysis virus (ALPV). The complete genome sequence of ALPV-Ir-Wi was 9824 nucleotides (nt) in length (excluding the 3′-poly(A) tail), and contained two ORFs, an intergenic untranslated region of 197 nt flanked by a 538 nt 5′ UTR and a 576 nt 3′ UTR. Comparison with 21 other ALPV genomic sequences from different parts of the world revealed that it most closely resembled the Turkish and Israeli isolates. Pairwise identity analysis showed significant variability in genome sequences among ALPV isolates with genomic nucleotide identities of 78.35–99.15%. In addition to codon mutations, insertions/deletions and recombination also contributed to genetic variability. To explore the genetic variation and molecular evolution of ALPV, ORF2 gene sequences of 18 non-recombinant isolates were analyzed. The isolates belonged to two principal clades (FST=0.614) and showed a considerable genetic diversity (0.140±0.01). Most populations were polyphyletic, indicating that they had not been isolated long enough to reach reciprocal monophyly. There was no significant correlation between genetic and geographical distances or host origins. Pairwise FST and Nm values showed a meaningful differentiation and relatively infrequent gene flow between two compared populations (the Middle East vs. East Asia, the Middle East vs. Africa), and moderate gene flow for East Asian and African populations. Genes in the ALPV genome were subject to strong purifying selection during evolution, and most codons were under negative selection or neutral evolution. The results indicated a relatively stable and conserved genomic composition with a low codon usage bias in all of the assayed ALPV coding sequences. Recombination, natural selection, gene flow, and founder effects were found to be the main evolutionary factors that can affect the genetic structure of ALPV populations.