Genomics and Applied Biology 2015, Vol. 6, No. 6, 1-7
1
Research Report Open Access
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
Corresponding author email
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: 10 Sep., 2015
© 2015 Khobondo et al., 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
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
1 Introduction
Pigs have been important in agriculture and welfare
for thousands of years. The recent completion of a
high-quality draft genome of
Sus scrofa
(Groenen et
al., 2012) enables the detailed investigation of a
variety of genomics features. For example, there are
attempts to link genotypic variation to phenotypic
variation in different animals including pigs. Advances in
molecular genetics from protein markers to single
nucleotide polymorphisms (SNPs) and copy number
variation (CNV) have shown drastic effects on phenotype
(Freeman et al., 2006) however, these types of variation
are unlikely to solely explain the large phenotypic
diversity found at the inter and intra specific level
(Paudel et al., 2013). Structural variations (SVs) like
copy number variations (CNVs) have shown to play a
prominent role in phenotypic evolution, adaptation
and domestication of pigs (Paudel et al., 2013).
Among the genetic variations, the advent of next
generation sequencing methods has further allowed
for a comprehensive screen of variation in codon
usage bias (CUB) preference. Studying the degeneracy
of genetic code, which enables most amino acids to be
coded by more than one codon called 'synonymous'
codon (Wright, 1990) has been done in pigs
(Khobondo et al., 2015). Huge interspecific and even
intragenomic variation in codon usage within and
between genomes has been documented as well (Jia et
al., 2009). Several biological factors such as tRNA
abundance (Kanaya et al., 2001), strand specific
mutational bias, replicational, transcriptional and
translational selection (Hershberg and Petrov, 2008),
secondary structure of proteins, mRNA structure, GC
composition (Knight et al., 2001), genomic
composition factors (Khobondo et al., 2015) and
environmental factors (Basak and Ghosh, 2005) have
been reported to influence the synonymous codon usage in
various organisms. The afore mentioned factors led to
two hypotheses on the evolution of codon bais;
mutation bias and natural selection for translation
accuracy and efficiency respectively (Sharp et al.,
2005). The mutational bias hypothesis predicts that
genes in the GC-rich regions of the genome
preferentially use G- and C-ending codons, while
those in the AT-rich regions use A- and T-ending
codons (Zhang et al., 2009) as observed in mammals.
