Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes

D. H.A. Fitch, L. D. Strausbaugh

Research output: Contribution to journalArticle

Abstract

We have evaluated codon usage bias in Drosophila histone genes and have obtained the nucleotide sequence of a 5.161-bp D. hydei histone gene repeat unit. This repeat contains genes for all five histone proteins (H1, H2a, H2b, H3, and H4) and differs from the previously reported one by a second EcoRI site. These D. hydei repeats have been aligned to each other and to the 5.0- kb (i.e., long) and 4.8-kb (i.e., short) histone repeat types from D. melanogaster. In each species, base composition at synonymous sites is similar to the average genomic composition and approaches that in the small intergenic spacers of the histone gene repeats. Accumulation of synonymous changes at synonymous sites after the species diverged is quite high. Both of these features are consistent with the relatively low codon usage bias observed in these genes when compared with other Drosophila genes. Thus, the generalization that abundantly expressed genes in Drosophila have high codon bias and low rates of silent substitution does not hold for the histone genes.

Original languageEnglish (US)
Pages (from-to)397-413
Number of pages17
JournalMolecular Biology and Evolution
Volume10
Issue number2
StatePublished - 1993

Keywords

  • Drosophila hydei
  • Drosophila melanogaster
  • codon optimization
  • histone genes
  • synonymous codon usage

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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