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Sensory rewiring in an echolocator: genome-wide modification of retinogenic and auditory genes in the bat Myotis davidii.

Hudson NJ, Baker ML, Hart NS, Wynne JW, Gu Q, Huang Z, Zhang G, Ingham AB, Wang L, Reverter A - G3 (Bethesda) (2014)

Bottom Line: Using the naked mole rat as a reference, we found five functional genes (CYP1A2, RBP3, GUCY2F, CRYBB1, and GRK7) encoding visual proteins that have degenerated into pseudogenes in M. davidii but not P. alecto.In a second approach genome-wide codon usage bias (CUB) was compared between the two bat species.Together, they help explain how natural selection has reduced physiological costs associated with the development of a smaller eye poorly adapted to day vision but that also contribute to enhanced dim light vision and the hearing adaptations consonant with echolocation.

View Article: PubMed Central - PubMed

Affiliation: Computational and Systems Biology, CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia nick.hudson@csiro.au.

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Genes showing extreme codon bias (negative differential entropy) on a within-genome basis in (A) M. davidii and (B) P. alecto, with those encoding vision and hearing related proteins highlighted.
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fig2: Genes showing extreme codon bias (negative differential entropy) on a within-genome basis in (A) M. davidii and (B) P. alecto, with those encoding vision and hearing related proteins highlighted.

Mentions: We calculated codon usage preferences for the two species genome-wide (Table 2 and Table 3). These genome-wide figures can be used to help establish preferred and nonpreferred codons for that particular species in concert with the available tRNA pool. In turn this helps shed light on the translational implications of CUB. Namely, is CUB likely to increase or decrease the energetic cost and efficiency of translation for the gene in question?


Sensory rewiring in an echolocator: genome-wide modification of retinogenic and auditory genes in the bat Myotis davidii.

Hudson NJ, Baker ML, Hart NS, Wynne JW, Gu Q, Huang Z, Zhang G, Ingham AB, Wang L, Reverter A - G3 (Bethesda) (2014)

Genes showing extreme codon bias (negative differential entropy) on a within-genome basis in (A) M. davidii and (B) P. alecto, with those encoding vision and hearing related proteins highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199690&req=5

fig2: Genes showing extreme codon bias (negative differential entropy) on a within-genome basis in (A) M. davidii and (B) P. alecto, with those encoding vision and hearing related proteins highlighted.
Mentions: We calculated codon usage preferences for the two species genome-wide (Table 2 and Table 3). These genome-wide figures can be used to help establish preferred and nonpreferred codons for that particular species in concert with the available tRNA pool. In turn this helps shed light on the translational implications of CUB. Namely, is CUB likely to increase or decrease the energetic cost and efficiency of translation for the gene in question?

Bottom Line: Using the naked mole rat as a reference, we found five functional genes (CYP1A2, RBP3, GUCY2F, CRYBB1, and GRK7) encoding visual proteins that have degenerated into pseudogenes in M. davidii but not P. alecto.In a second approach genome-wide codon usage bias (CUB) was compared between the two bat species.Together, they help explain how natural selection has reduced physiological costs associated with the development of a smaller eye poorly adapted to day vision but that also contribute to enhanced dim light vision and the hearing adaptations consonant with echolocation.

View Article: PubMed Central - PubMed

Affiliation: Computational and Systems Biology, CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia nick.hudson@csiro.au.

Show MeSH
Related in: MedlinePlus