On the limitations of using ribosomal genes as references for the study of codon usage: a rebuttal.
other · Level V
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- Record sourced from PubMed, PMID 23284622.
- Also identified by DOI 10.1371/journal.pone.0049060 and PMC identifier PMC117187.
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Abstract
In a recent paper published in PLOS ONE, Wang et al. challenge our finding that the identity of optimal codons in different genomes follows a set of clear rules. Here we provide a rebuttal of their paper and demonstrate that the results of our original PLOS Genetics paper stand. This provides us with an opportunity to bring up an aspect of how codon usage has been studied that should be of general interest. The Wang et al. study, as well as many other studies, used ribosomal genes as a reference set for the study of patterns of codon usage. We discuss here the assumptions that are made in order to justify using ribosomal genes to study codon bias, suggest that this practice can at times be problematic, and discuss its limitations.