Prediction of codon bias in rice (Oryza sativa) genes
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Date
2012
Authors
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Journal ISSN
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Publisher
CCSHAU
Abstract
Patterns and degrees of codon usage bias vary not only among different organisms, but also
among genes in the same organism. Codon usage bias (CUB) conveys useful information about the
selection on synonymous codons induced by gene expression, translation efficiency and about the
distinctive evolutionary properties. In the present study, by using 28502 complete coding sequences
(CDS) of rice (Oryza sativa) with full length cDNA support, a detailed analysis of the codon bias was
performed by employing Automated Codon Usage Analysis (ACUA) tool. 27897 genes demonstrated
codon bias as their ENc (effective number of codons) values varied from 20 to less than 61. On basis of
GC3
content values, 267 biased genes were taken as high GC
3(GC3>=0.8) whereas 27630 biased genes
were termed as low GC3(GC3
<0.8) genes. Quantification of genomic compositional asymmetry and
dinucleotide frequency distribution analysis were further performed on selected biased genes to provide
possible reasons of differences in nucleotide composition and compositional gradients along the coding
regions of all the genes. GC3
gradient analysis results revealed that from the 5' end to 3' end of the open
reading frame, high GC3
biased genes had a very slight positive gradient and low GC
3biased genes had
strong negative gradient. CG3 skewness analysis showed that C3 preference even though higher for
high GC
3genes than low GC
3genes, varied differentially as a function of distance from ATG codon.
The analysis for CG3- and GC3- skewness as a function of distance from the startcodon in rice genes
clearly depicted the prevailing tendency for GC
3 to decrease toward the 3' end. By dinucleotide
frequencies ratio distribution analysis, 45/267 high GC
3 biased genes were detected at CG/GC
dinucleotide frequencies ratio peak centered at 1.1, whereas 1729/27630 and 1762/27630 low GC3
genes with CG/GC dinucleotide frequencies ratio peaks centered at 0.5 and 1.1, respectively were
observed that clearly depicted that high GC
3 genes had a significantly higher frequency of CG
dinucleotides than low GC
3genes. The differential pattern of GC
3bias in rice genes shown in our study
corroborate with the previous studies that plant codon usage might be affected by translational
selection.
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Keywords
Animal husbandry, Livestock, Mastitis, Lactation, Economic systems, Byproducts, Yields, Biological phenomena, Seasons, Animal developmental stages