Genomics and Applied Biology 2015, Vol. 6, No. 6, 1-7
6
biased in olfactory receptors (OR) was expected.
Sus
scrofa
have the largest repertoire of functional OR
genes in mammals whose genome has been sequenced
to date (Nguyen et al., 2012), likely related to the
strong dependence on their sense of smell for foraging
especially in wild and in extensive production system.
For efficiency of foraging different feeds, high
flexibility of codon usage is thus justified. There are
about 1301 porcine OR genes, nearly a third are found
as copy number variable in pigs. Such large numbers
of genes are less conserved and might explain the low
CUB as reported in this study. These findings suggest
that the wide variety of environmental conditions
faced by pigs around the world have resulted in low
CUB for flexibility and high CNVs. This low CUB
could be because these genes are less conserved and
need to evolve fast to adapt to ever changing antigenic
determinants and artificially created environment for
immune and olfactory receptor genes respectively.
Cell apoptosis through fas ligand (Griffith et al., 1995)
being the principal mechanism by which the majority
of effecter T and B lymphocytes die after clearance of
an infection may justify the low CUB witnessed in this
study. This might be to meet the changing infection-
clearance status to regulate uncontrolled activation of
lymphocytes that may result to self-destruction, limit auto
reactivity and bring forth immune tolerance.
Conclusion
Functional analyses revealed high and low codon
usage bias enriched with genes related to housekeeping
functions and immune, sensory perception and response
to stimulus respectively.
Authors’ contributions
Khobondo J.O. conceived and designed the experiments,
developed perl script, wrote the manuscript; Kahi A.K.
discussed and improved manuscript; Ngeno K. analysed the
data, improved the manuscript. All authors read and approved
the final manuscript.
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