Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

Plants, Год журнала: 2024, Номер 13(4), С. 468 - 468

Опубликована: Фев. 6, 2024

Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 from four cruciferous species, Arabidopsis thaliana, Brassica napus, rapa, Camelina sativa, that were Ensembl plants database, we subsequently investigated their CUB. As result, base composition analysis revealed overall GC content was below 50%. The significantly correlated with constituents at three positions, implying both mutation pressure natural selection might contribute to relatively high ENc values suggested CUB species weak. Subsequently, exhibited negative correlation gene expression levels. Analyses, including ENc-plot analysis, neutral PR2 bias, mainly shaped patterns these species. In addition, total 12 optimal codons (ΔRSCU > 0.08 RSCU 1) across A neighbor-joining phylogenetic based on coding sequences (CDS) showed strictly distinctly clustered into subfamilies. Principal component cluster relative synonymous (RSCU) supported fact pattern consistent genetic relationship level (or) These results will not only enrich resource also advance our understanding genes, which may underlie theoretical basis for exploration evolutionary pattern.

Язык: Английский

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SARS-CoV-2 CoCoPUTs: Analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multi-year period

Virus Evolution, Год журнала: 2025, Номер 11(1)

Опубликована: Янв. 1, 2025

A consistent area of interest since the beginning severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been sequence composition virus and how it changed over time. Many resources have developed for storage analysis SARS-CoV-2 data, such as GISAID (Global Initiative on Sharing All Influenza Data), NCBI, Nextstrain, outbreak.info. However, relatively little done to compile codon usage codon-level mutation secondary structure data into a single database. Here, we assemble aforementioned many additional attributes in new database entitled CoCoPUTs. We begin with an overview overlap between two largest sources data: NCBI Virus (GenBank). then evaluate different types curation strategies reduce dataset millions sequences only one per Pango lineage variant. performed specific analyses coding (CDSs), including calculating usage, pair dinucleotides, junction mutations, GC content, effective number codons (ENCs), pairs (ENCPs). also whole-genome RNA prediction calculations each variant, using LinearPartition software modified selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) that are available online. Finally, compiled all our resource, CoCoPUTs, paired resulting statistics variant proportion time order derive trends viral evolution. Although overall did not change drastically, line previous literature this subject, observe while GC% content decreased, third position was more positive relative February 2021 July 2023. Over same interval, noted both synonymous nonsynonymous mutations increased number, outpacing at rate 3:1. predicted structures nearly contained previously described virus-activated inhibitor translation (VAIT) stem loops, validating first their existence variants (as opposed local predictions). separately produced mutation-deprived set repeated set. This revealed interesting trend reduced ensemble free energy compared unaltered structures, indicating play role increasing molecules. These validate studies describing increases human viruses indicate possible biology.

Язык: Английский

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Analysis of synonymous codon usage bias of Lassa virus

Virus Research, Год журнала: 2025, Номер 353, С. 199528 - 199528

Опубликована: Янв. 29, 2025

Lassa virus genome consists of two single-stranded, negative-sense RNA segments that lie in the genus Arenavirus. The disease associated with is distributed all over world, approximately 3,000,000-5,000,000 infections diagnosed annually West Africa. It shows high health risks to human being. Previous research used evolutionary time scale and adaptive evolution describe population pattern. However, it still unclear how takes advantage synonymous codons. In this study, we analyzed codon usage bias 162 strains by calculating comparing nucleotide contents, effective number codons (ENC), adaptation index (CAI), relative (RSCU), others. results disclosed LASV are rich A/T. average ENC value indicated a low LASVs. ENC-plot, neutrality plot parity rule 2 demonstrated that, besides mutational pressure, other factors like natural selection also contributed bias. This study significant because described pattern genomes viruses provided information needed for fundamental them.

Язык: Английский

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Comparative genetic analysis of pathogenic and attenuated strains of Junín virus

Genetica, Год журнала: 2025, Номер 153(1)

Опубликована: Фев. 8, 2025

Язык: Английский

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Natural selection pressure exerted on “Silent” mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure

Virus Research, Год журнала: 2022, Номер 323, С. 198966 - 198966

Опубликована: Окт. 14, 2022

From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, were regarded as "silent" received less attention than cause amino acid variations. However, importance can not be neglected. This research focuses on SARS-CoV-2 proves under purifying selection in its evolution. The evidence is provided by comparing mutation number per site coding non-coding regions. We then study two forces selection: codon usage RNA secondary structure. Results show optimization leads to an adapted towards humans. Furthermore, our results maintenance structure causes structural region. These explain pressure during evolution SARS-CoV-2.

Язык: Английский

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Natural Selection Primarily Shaping Codon Usage Bias in Glycine max (soybean) WRKY Genes

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Май 29, 2024

Background: Codon usage biases in genomes emerge from the interaction of two prominent evolutionary factors: mutational pressure and natural selection. Studying codon bias facilitates understanding fundamental mechanisms influencing genetic structure. Glycine max (soybean) holds considerable agricultural industrial significance as a widely cultivated crop. Despite pivotal role WRKY transcription factors plant regulation stress responses, investigations these are limited, providing an opportunity to probe trends within this gene family. Results: Examination base composition genes revealed average GC content 44.85% GC3 42.01%, indicating preference for A/T(U)-ending codons. Relative synonymous (RSCU) analysis identified 27 codons with RSCU > 1, predominantly ending A U bases. The effective number (N_C) ranged 42.17 61, adaptation index (CAI) values ranging 0.713 0.904, suggesting phenomenon weak yet high expression levels genes. Neutrality indicated significantly correlation between GC12 GC3, while N_C plot predominant selection shaping pattern. Parity rule 2 (PR2) highlighted disproportionate AT One optimal was identified. Conclusion: Natural is primary driving force preferences These findings provide new insights into landscape translational efficiency max, contributing enhancement resources soybeans.

Язык: Английский

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Natural selection shapes codon usage and host adaptation of NS1 in mosquito-borne pathogenic flaviviruses

International Journal of Biological Macromolecules, Год журнала: 2024, Номер 292, С. 139187 - 139187

Опубликована: Дек. 28, 2024

Язык: Английский

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Human Riboviruses: A Comprehensive Study

Journal of Molecular Evolution, Год журнала: 2024, Номер unknown

Опубликована: Дек. 31, 2024

Язык: Английский

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Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness

Archives of Virology, Год журнала: 2022, Номер 167(12), С. 2677 - 2688

Опубликована: Сен. 27, 2022

Язык: Английский

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Impact of different synonymous codon substitution strategies on SARS-CoV-2 nucleocapsid protein expression in Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 7, 2024

Abstract SARS-CoV-2 is an enveloped, positive-strand RNA virus. The virus nucleocapsid (N) protein stable, conserved, highly immunogenic, and less prone to mutation during infection, making it a key antigen in vitro diagnosis, vaccine development, immunological structural studies. synonymous codon substitution, gene engineering method synthetic biology the approach improve composition of recombinant based on various criteria without altering amino acid sequence. We analyzed influence different substitution strategies N-protein expression E. coli . Using JCat Genewiz optimization tools, harmonization (CH) tool, we predicted compared how parameters such as GC content, Codon Adaptation Index, quality number rare codons present these sequences affect expression. Our prediction also shows that Minimum Free Energy (MFE) structure N-term C-tail coding sequence folding. demonstrated SR-rich region may contribute slowing down elongation rate translation. In general, better result from our analysis. This work presents fundamental analysis tools folding suggests basic choosing best strategy for optimal further Key points affects Parameters impact variation structures stability, slow predicts rhythm pattern.

Язык: Английский

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