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

David Fitch, Linda 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 - Mar 1993

Fingerprint

Drosophila hydei
histones
codons
Codon
Histones
Drosophila
Drosophila melanogaster
substitution
Substitution reactions
Genes
gene
genes
Melanogaster
rate
Base Composition
Chemical analysis
intergenic DNA
genomics
Nucleotides
nucleotide sequences

Keywords

  • Codon optimization
  • Drosophila hydei
  • Drosophila melanogaster
  • Histone genes
  • Synonymous codon usage

ASJC Scopus subject areas

  • Agricultural and Biological Sciences (miscellaneous)
  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Genetics
  • Molecular Biology
  • Genetics(clinical)

Cite this

Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes. / Fitch, David; Strausbaugh, Linda D.

In: Molecular Biology and Evolution, Vol. 10, No. 2, 03.1993, p. 397-413.

Research output: Contribution to journalArticle

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