Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton. This phenomenon is thought to be driven by selection for trans...
Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak sele...
Xyloglucan endotransglycosylase (XET) genes are widely distributed in most plants, but the codon usage bias of XET genes has remained uncharacterized. Thus, we analyzed the codon usage bias using 4500 codons of 20 XET genes to elucidate the genetic a...
Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of...
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major...
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection te...
Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for op...
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...
The plant Actinostemma tenerum is endemic to East Asia and has been used as a traditional medicinal herb for over 1400 years. Investigating the chloroplast genome characteristics and codon usage bias (CUB) is essential for advancing research on molec...
Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes...
The codon usage bias (CUB) of genes encoded by different species’ genomes varies greatly. The analysis of codon usage patterns enriches our comprehension of genetic and evolutionary characteristics across diverse species. In this study, we perf...
Synonymous codon usage (codon bias) greatly influences not only translation but also mRNA stability. In vertebrates, highly expressed genes preferentially use codons with an optimal tRNA adaptation index (tAI) that mostly end in C or G. Surprisingly,...
3 September 2024
In order to understand the bias and main affecting factors of codon usage in the plastid genome of Diplandrorchis sinica, which is a rare and endangered plant species in the Orchidaceae family, the complete plastid genome sequence of D. sinica was do...
Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in...
Milk production is an essential economic trait in cattle, and understanding the genetic regulation of this trait can enhance breeding strategies. The discoidin domain receptor 1 (DDR1) gene has been identified as a key candidate gene that influences...
Codon usage bias (CUB) refers to the different frequencies with which various codons are utilized within a genome. Examining CUB is essential for understanding genome structure, function, and evolution. However, little was known about codon usage pat...
Background: Siphonaria is a genus of false limpets belonging to the Gastropoda class. Only two species of this genus have been described with mitochondrial genomes. Moreover, the codon usage patterns and factors influencing them have not been studied...
Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging bat-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in human beings. Despite the fatal nature of t...
Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias e...
Tea, a widely consumed beverage globally, is a vital agricultural product for many countries. Polyphenol oxidases (PPOs), copper-containing enzymes found in plants, fungi, and animals, are essential for physiological metabolism and enzymatic browning...
Background: The codon preference of chloroplast genomes not only reflects mutation patterns during the evolutionary processes of species but also significantly affects the efficiency of gene expression. This characteristic holds significant scientifi...
Codon usage bias (CUB) phenomenon varies with the species and even within the genes of the same species, where few codons are preferred more frequently than their other synonymous codons. It also categorizes the differences between species. Nucleotid...
Objectives: Codon usage bias is a fundamental feature of gene expression that can influence evolutionary processes and genetic diversity. This study aimed to investigate the mitochondrial codon usage characteristics and their driving forces in three...
Background:Ants are among the most widely distributed eusocial insects, and desert ants, in particular, serve as important model organisms for studying animal navigation. Methods: In this study, we provide high-quality de novo transcriptomes for eigh...
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 genes from four cruciferous species, Arabidopsi...
Background/Objectives: In order to determine the basic structural characteristics of the mitochondrial genome of Cyphochilus crataceus and explore its phylogenetic status, as well as to understand the codon usage bias of Melolonthinae species, the ne...
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential...
The Boraginales (Boraginaceae a.l.) comprise more than 2450 species worldwide. However, little knowledge exists of the characteristics of the complete plastid genome. In this study, three new sequences representing the first pt genome of Heliotropiac...
Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of H...
Background: Cavariella salicicola (Hemiptera: Aphidinae) is a pest on Salix spp. and various Umbelliferae (Apiaceae) vegetables. However, the taxonomic status and phylogenetic relationship of the genus Cavariella within Aphidinae remain controversial...
Tarantulas (family Theraphosidae) are ecologically significant invertebrate predators in terrestrial ecosystems, but many species face threats from habitat fragmentation and unsustainable collection for the international pet trade. Brachypelma albice...
Solanum is one of the largest genera, including two important crops—potato (Solanum tuberosum) and tomato (Solanum lycopersicum). In this study we compared the chloroplast codon usage bias (CUB) among 12 Solanum species, between photosynthesis-relate...
Biebersteiniaceae and Nitrariaceae, two small families, were classified in Sapindales recently. Taxonomic and phylogenetic relationships within Sapindales are still poorly resolved and controversial. In current study, we compared the chloroplast geno...
Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-do...
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 res...
Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolut...
Citrus leaf blotch virus (CLBV) is a positive-sense single-stranded RNA virus belonging to the genus Citrivirus within the family Betaflexiviridae. It infects a broad range of economically significant fruit crops, including citrus, kiwifruit, and app...
Background: Ulva is a globally distributed genus with ecological and economic significance, yet the codon usage bias of the Ulva chloroplast genome remains poorly understood. Methods: We assessed the Ulva chloroplast genome codon usage patterns and t...
Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including comp...
The tRNA epitranscriptome has been recognized as an important player in mRNA translation regulation. Our knowledge of the role of the tRNA epitranscriptome in fine-tuning translation via codon decoding at tissue or cell levels remains incomplete. We...
Synonymous codon usage (SCU) bias in oil-tea camellia cpDNAs was determined by examining 13 South Chinese oil-tea camellia samples and performing bioinformatics analysis using GenBank sequence information, revealing conserved bias among the samples....
Chloroplast codon usage bias (CUB) records both maternal phylogeny and selection intensity. Characterizing CUB in the synthetic cereal × Triticosecale and its Triticum and Secale parents is therefore a prerequisite for plastid-based engineering...
Porcine reproductive and respiratory syndrome virus (PRRSV) is economically important and characterized by its extensive variation. The codon usage patterns and their influence on viral evolution and host adaptation among different PRRSV strains rema...
All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, e...
Tomato spotted wilt virus (TSWV), belonging to the genus Orthotospovirus, is a significant pathogen through its infection of economically vital crops including tomato, tobacco, pepper, and other species worldwide. Given its substantial influence on t...
Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patte...
Brachypodium distachyon, a new monocotyledonous model plant, has received wide attention in biological research due to its small genome and numerous genetic resources. Codon usage bias is an important feature of genes and genomes, and it can be used...
The non-random usage of synonymous codons encoding the same amino acid—referred to as codon usage bias (CUB)—varies substantially across genomes and significantly affects translational efficiency by modulating transcriptional and post-tra...
Codon bias analysis of SARS-CoV-2 reveals suboptimal adaptation for translation in human cells it infects. The detailed examination of the codons preferentially used by SARS-CoV-2 shows a strong preference for LysAAA, GlnCAA, GluGAA, and ArgAGA, whic...
Codon usage bias, which exists in many genomes, is mainly determined by mutation and selection. To elucidate the genetic features and evolutionary history of herbaceous peony (Paeonia lactiflora), a well-known symbol of prosperity in China, we examin...
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