ArticleBMC genomics2015
Non-uniqueness of factors constraint on the codon usage in Bombyx mori.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed.
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- Mitochondrial codon usage bias and novel phylogenetic insights: implications for taxonomic reevaluation of seven Xylotini species (Diptera, Syrphidae, Eristalinae).BMC genomics · 2025Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
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- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution.BMC genomics · 2025Article
- Analysis of Codon Usage Bias in the Plastid Genome ofCurrent issues in molecular biology · 2024Article
- Comparative analysis of the organelle genomes of Aconitum carmichaelii revealed structural and sequence differences and phylogenetic relationships.BMC genomics · 2024Article
- Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of FourGenes · 2023Article
- Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses.Frontiers in immunology · 2023Article
- Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses.Genes & genomics · 2022Article
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- Codon usage patterns across seven Rosales species.BMC plant biology · 2022Article
- Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns.Frontiers in neuroscience · 2022Article
- Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori.
resultsA total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans).
conclusionsThe codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the "optimal codons" of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.
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