Patterns of codon usage bias in three dicot and four monocot plant species.

Kawabe, Akira; Miyashita, Naohiko T.

doi:10.1266/ggs.78.343

Cited by 173 publications

(139 citation statements)

References 34 publications

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“…The other defines optimal codons as those showing a statistically significant increase in frequency between genes with low-and high-codon usage bias (Stenico et al, 1994). To determine the optimal codon, the low and high bias or expression datasets of genes are assessed through multiple methods, such as CAI, ENC, expressed sequence tag counts, and transfer RNA gene copy number (Kawabe and Miyashita, 2003;Liu et al, 2004;Mukhopadhyay et al, 2007b). Our study evaluated one major trend in the first axis, which can account for 46.65% of the total variation and explain approximately 10 times as much of the variation as that explained by the second and subsequent axes.…”

Section: Discussionmentioning

confidence: 99%

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Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Liu

Huang²,

Du³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that lowand high-GC content genes with different codon usage occur frequently in the genome. The results of neutrality, correspondence, and correlation analyses indicated that mutational pressure and selective constraint were the main factors in shaping codon usage. Coding sequence length and the hydrophobicity of each protein were also identified as influences on codon usage bias, although their effect was minor. In addition, 27 codons, defined as "optimal codons", might provide useful information for gene engineering, gene prediction, and molecular evolution studies.

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Section: Discussionmentioning

confidence: 99%

“…To investigate the nucleotide composition of Brachypodium genes, we computed the GC content of the entire concatenated sequence and each gene (Kawabe and Miyashita, 2003). We concatenated all genes to one sequence, which comprised 10,908,249 codons.…”

Section: Nucleotide Compositional Constraint Analysismentioning

confidence: 99%

Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Liu

Huang²,

Du³

et al. 2012

Genet. Mol. Res.

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“…As a measure of codon usage bias, the effective number of codons (ENC: Wright 1990) was estimated. Percentage of the preferred codons (Akashi and Schaeffer 1997) in the MT genes was determined based on Kawabe and Miyashita (2003). Linkage disequilibrium between DNA sequence variants (site and indel) was examined using Chi-square test.…”

Section: Materials and Metodsmentioning

confidence: 99%

DNA variation in the metallothionein genes in wild rice Oryza rufipogon: Relationship between DNA sequence polymorphism, codon bias and gene expression

2005

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This study examines the relationship between DNA sequence variation and level of gene expression in four metallothionein genes from wild rice Oryza rufipogon . The nucleotide diversity was 0.0028 to 0.0117 over the entire coding and non-coding region, and it was negatively correlated with gene expression for three type 2 metallothionein genes. In contrast, codon bias and percent of preferred codons correlated positively with gene expression. These results indicate that the intensity of natural selection depends on the level of gene expression, which in turn shapes the level of nucleotide polymorphism. In addition, significant linkage disequilibria were frequent between the metallothionein genes, although significance was not confirmed after multiple test correction. This result suggests that metallothionein genes expressed at different levels are epistatic with respect to fitness, and that gene expression is an important factor determining level of DNA polymorphism.

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“…nl/). The GC12 value was calculated as the mean of GC1 and GC2, and it was used for neutrality analyses (Kawabe and Miyashita, 2003).…”

Section: Synonymous Codon Usage Bias In L Japonicus Nbs-encoding Genesmentioning

confidence: 99%

Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

Song

Wang

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Nucleotide-binding site (NBS) disease resistance genes play a crucial role in plant defense responses against pathogens and insect pests. Many NBS-encoding genes have been detected in Lotus japonicus, an important forage crop in many parts of the world. However, most NBS genes identified so far in L. japonicus were only partial sequences. We identified 45 full-length NBS-encoding genes in the L. japonicus genome, and analyzed gene duplications, motifs, and the molecular phylogeny to further understand the NBS gene family. We found that gene duplication events rarely occur in L. japonicus NBS-encoding (LjNBS) genes. In addition, LjNBS genes were subjected to selection pressure, and codon usage bias was evident. We tested for purifying selection (specifically in the CC-NBS-LRR and TIR-NBS-LRR groups), and found strong purifying selection in the TIR-domain-containing sequences, indicating that the CC-NBS-LRR group is more likely to undergo expansion than the TIR-NBS- LRR group. Moreover, our results showed that both selection and mutation contributed to LjNBS codon usage bias, but mutational bias was the major influence on codon usage.

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Patterns of codon usage bias in three dicot and four monocot plant species.

Cited by 173 publications

References 34 publications

Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

DNA variation in the metallothionein genes in wild rice Oryza rufipogon: Relationship between DNA sequence polymorphism, codon bias and gene expression

Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

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