Articles
Analysis of codon usage patterns of CYP genes superfamily in pomegranate
Article number
1254_5
Pages
27 – 34
Language
English
Abstract
The cytochrome P450 (CYP) superfamily is the largest enzymatic family in plants, and regulates numerous key cell processes that affect plant growth and development.
As one of the oldest known edible fruit tree species, the codon usage pattern analysis of pomegranate CYP superfamily is a good genetic tool to understand its evolutionary and genetic mechanisms.
In this study, a total of 83 CYP homologous genes were isolated from a pomegranate transcriptome employing Illumine RNA-seq technology.
Meanwhile, the codon composition and usage bias of CYP genes for pomegranate were analyzed to investigate codon usage patterns and factors affecting codon usage.
The effective number of codons (ENC) varies from 37.41 to 58.73, with a mean value of 50.45 and a standard deviation (SD) of 5.62, revealing that there is only a weak codon bias.
An ENC-GC3 scatter diagram indicates that conditional mutation might be a factor in determining the codon bias, but there still exist some others.
Significantly positive correlation (r=0.941, P<0.001) of GC was observed with GC3, which may be due to the effect of compositional constraint arising from mutation pressure.
Neutrality plot elucidates that natural selection together with some other minor factors play a dominate role in affecting codons usage patterns of pomegranate CYP genes.
Moreover, the 19 most frequently used codons were observed and all of them ended by G and C, which enables to shed some light on enhancing the heterologous genes expression of CYP in Punica granatum L. through codon optimization.
As one of the oldest known edible fruit tree species, the codon usage pattern analysis of pomegranate CYP superfamily is a good genetic tool to understand its evolutionary and genetic mechanisms.
In this study, a total of 83 CYP homologous genes were isolated from a pomegranate transcriptome employing Illumine RNA-seq technology.
Meanwhile, the codon composition and usage bias of CYP genes for pomegranate were analyzed to investigate codon usage patterns and factors affecting codon usage.
The effective number of codons (ENC) varies from 37.41 to 58.73, with a mean value of 50.45 and a standard deviation (SD) of 5.62, revealing that there is only a weak codon bias.
An ENC-GC3 scatter diagram indicates that conditional mutation might be a factor in determining the codon bias, but there still exist some others.
Significantly positive correlation (r=0.941, P<0.001) of GC was observed with GC3, which may be due to the effect of compositional constraint arising from mutation pressure.
Neutrality plot elucidates that natural selection together with some other minor factors play a dominate role in affecting codons usage patterns of pomegranate CYP genes.
Moreover, the 19 most frequently used codons were observed and all of them ended by G and C, which enables to shed some light on enhancing the heterologous genes expression of CYP in Punica granatum L. through codon optimization.
Authors
M. Yan, T.K. Zhang, Z.H. Yuan
Keywords
Punica granatum, CYP genes, codon usage bias
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