Structure and sequence of the Cu, Zn superoxide dismutase gene of Chymomyza amoena: phylogeny of the genus and codon-use evolution

We have cloned and sequenced the Cu, Zn superoxide dismutase gene of Chymomyza amoena. The coding sequence has the same length as in Drosophila species and in Ceratitis capitata. There are two introns, located at the same sites as in Ceratitis. The second intron is absent in Drosophila: this places Chymomyza outside the Drosophila lineage, contrary to proposals based on anatomical and other evidence. The nucleotide or amino acid distances support a phylogeny in which Ceratitis first branches off the common stem, then Chymomyza splits before the divergence of the two major Drosophila subgenera. The estimated divergence times are 58 million for Chymomyza-Drosophila; 48 million years for the Drosophila subgenera. During the intervening 10 million years, the Drosophila lineage lost the second intron and evolved distinct codon-preferences: the G + C use in the third coding positions is increased by 69% in Drosophila relative to Chymomyza or Ceratitis.