ArticleMolecular biology reports2010
Analysis of synonymous codon usage in Zea mays.
Article in Molecular biology reports, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 107 citations in OpenAlex.
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- Comparative Analysis of Codon Usage Bias in Transcriptomes of Eight Species of Formicidae.Genes · 2025Article
- Codon usage bias analysis of theFrontiers in genetics · 2025Article
- Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.International journal of molecular sciences · 2024Article
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- Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae.BMC plant biology · 2024Article
- The complete Chloroplast genome of Stachys geobombycis and comparative analysis with related Stachys species.Scientific reports · 2024Article
- Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae).BMC genomics · 2024Article
- An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea.BMC genomic data · 2023Article
- Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.International journal of molecular sciences · 2023Article
- The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family.Genomics & informatics · 2022Article
- An investigation of codon usage pattern analysis in pancreatitis associated genes.BMC genomic data · 2022Article
- Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus.BMC genomic data · 2022Article
- Genome-wide analysis of codon usage in sesame (Heliyon · 2022Article
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- Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana.Scientific reports · 2021Article
- Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species.Frontiers in genetics · 2021Article
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Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is important and meaningful to understand the codon usage pattern and the factors that shape codon usage of maize. In this study, trends in synonymous codon usage in maize have been firstly examined through the multivariate statistical analysis on 7402 cDNA sequences. The results showed that the genes positions on the primary axis were strongly negatively correlated with GC3s, GC content of individual gene and gene expression level assessed by the codon adaptation index (CAI) values, which indicated that nucleotide composition and gene expression level were the main factors in shaping the codon usage of maize, and the variation in codon usage among genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. At the same time, CDS length and the hydrophobicity of each protein were, respectively, significantly correlated with the genes locations on the primary axis, GC3s and CAI values. We infer that genes length and the hydrophobicity of the encoded protein may play minor role in shaping codon usage bias. Additional 28 codons ending with a G or C base have been defined as "optimal codons", which may provide useful information for maize gene-transformation and gene prediction.
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