ArticleInternational journal of molecular sciences2016
Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae.
Article in International journal of molecular sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
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- Composition and Codon Usage Pattern Results in Divergence of theJournal of fungi (Basel, Switzerland) · 2022Article
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- Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens.Molecular genetics and genomics : MGG · 2021Article
- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago.World journal of microbiology & biotechnology · 2019Article
- Codon usage vis-a-vis start and stop codon context analysis of three dicot species.Journal of genetics · 2018Article
- Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis.Frontiers in plant science · 2018Article
- Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution.Microbial pathogenesis · 2017Article
- Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi.Scientific reports · 2017Article
- Comprehensive Analysis of Codon Usage Bias in SevenFrontiers in microbiology · 2017Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.
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