Linking codon usage bias to functional genomics in pigs  

Khobondo  J. O. , Ngeno  K. , Kahi  A. K.
Animal Breeding and Genomics Group, Department of Animal Sciences, Egerton University, PO Box 536 -20115 Egerton. Kenya
Author    Correspondence author
Genomics and Applied Biology, 2015, Vol. 6, No. 6   doi: 10.5376/gab.2015.06.0006
Received: 15 Jul., 2015    Accepted: 16 Aug., 2015    Published: 15 Sep., 2015
© 2015 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Khobondo J. O., Ngeno K. and Kahi A.K., 2015, Linking codon usage bias to functional genomics in pigs, Genomics and Applied Biology, Vol.6, No.6, 1-7 (doi: 10.5376/gab.2015.06.0006)

Abstract

The recent completion of a high-quality draft genome of Sus scrofa has enabled the detailed investigation of a variety of genomics features. There have been attempts to link genotypic variation to phenotypic variation in different animals including pigs using single nucleotide polymorphisms, copy number variation and decipher codon usage bias. The prevalence of codon usage has never been ascertained in any animal, this study therefore link codon usage bias to gene ontology enrichment. The genome CDS sequence was downloaded from Ensemble v68 Sus scrofa build 10.2 using BioMart (Ensembl v68). A total of 21,550 CDS with more than 50 amino acids (150 bp) were used to derive genomic codon adaptation index (proxy for codon usage bias) using an in house built perl script. Five percent low and highly codon usage biased gene were extracted. BinGO v2.44 within Cytoscape v.2.8.3 was used to identify enriched gene ontology terms using human gene annotation as background and validated by perl script. Gene ontology terms related to immune response and sensory perception were linked to lowly codon usage bias. The highly codon usage bias genes were overrepresented in gene ontology terms involved in housekeeping functions of cells. Codon usage bias controls functional genomics.

Keywords
Codon usage; Gene enrichment; Functional genomic; Pigs
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