The Effect of Local Nucleotides on Synonymous Codon Usage in the Honeybee (<Emphasis Type="Italic">Apis mellifera</Emphasis> L.) Genome |
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Authors: | Robert W Cutler Panuwan Chantawannakul |
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Institution: | (1) Department of Biology, Bard College, Annandale-on-Hudson, NY 12504, USA;(2) Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand |
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Abstract: | Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that
affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third
codon site are correlated, dependent on their weak (adenine A] or thyamine T]) versus strong (guanine G] or cytosine C]) status, to nucleotides on the first codon site which are dependent on their purine (A/G) versus pyrimidine (C/T) status. In particular, for adjacent third and first site nucleotides, weak–pyrimidine and strong–purine nucleotide combinations
occur much more frequently than the underabundant weak–purine and strong–pyrimidine nucleotide combinations. Since a similar
effect is also found in the noncoding regions, but is present for all adjacent nucleotides, this coding effect is most likely
due to a genome-wide context-dependent mutation error correcting mechanism in combination with selective constraints on adjacent
first and second nucleotide pairs within codons. The position-dependent relationship of synonymous codon usage is evidence
for a novel form of codon position bias which utilizes the redundancy in the genetic code to minimize the effect of nucleotide
mutations within coding regions.
Reviewing Editor: Dr. Brian Morton] |
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Keywords: | Honeybee genome Dinucleotide frequency Genomics Synonymous codon usage Apis mellifera Bioinformatics Base context |
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