Genomic composition factors affect codon usage in porcine genome

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  • J O Khobondo, Animal Breeding and Genomics Group, Department of Animal Sciences, Egerton University, Kenya
  • Tobias O Okeno, Animal Breeding and Genomics Group, Department of Animal Sciences, Egerton University, Danmark
  • A K Kahi, Animal Breeding and Genomics Group, Department of Animal Sciences, Egerton University, Kenya
The objective of the study was to determine the codon usage bias in the porcine genome and decipher its determinants. To investigate the underlying mechanisms of codon bias, the coding sequence (CDS) from the swine reference sequence (ssc10.2) was extracted using Biomart. An in house built Perl script was used to derive various genomic traits and codon indices. Analysis was done using R statistical package, and correlations and multivariate regressions were performed. We report the existence of codon usage bias that might suggest existence of weak translational selection. The codon bias is feebly related to nucleotide composition (GC%, GC3, CDS length). This study can be explored for designing degenerate primers, necessitate selecting appropriate hosts expression systems to manipulate the expression of target genes in vivo or in vitro and improve the accuracy of gene prediction from genomic sequences thus maximizing the effectiveness of genetic manipulations in synthetic biology
OriginalsprogEngelsk
Artikelnummer886C72649965
TidsskriftAfrican Journal of Biotechnology
Vol/bind14
Nummer4
Sider (fra-til)341-349
Antal sider9
ISSN1684-5315
DOI
StatusUdgivet - 2015

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