Synonymous Substitutions in the Xdh Gene of Drosophila: Heterogeneous Distribution Along the Coding Region

Abstract

The Xdh (rosy) region of Drosophila subobscura has been sequenced and compared to the homologous region of D. pseudoobscura and D. melanogaster. Estimates of the numbers of synonymous substitutions per site (Ks) confirm that Xdh has a high synonymous substitution rate. The distributions of both nonsynonymous and synonymous substitutions along the coding region were found to be heterogeneous. Also, no relationship has been detected between Ks estimates and codon usage bias along the gene, in contrast with the generally observed relationship among genes. This heterogeneous distribution of synonymous substitutions along the Xdh gene, which is expression-level independent, could be explained by a differential selection pressure on synonymous sites along the coding region acting on mRNA secondary structure. The synonymous rate in the Xdh coding region is lower in the D. subobscura than in the D. pseudoobscura lineage, whereas the reverse is true for the Adh gene.

The Hill–Robertson effect is a consequence of interplay between linkage, selection and drift: a commentary on ‘The effect of linkage on limits to artificial selection’ by W. G. Hill and A. Robertson

“…309-310. f 2008 Cambridge University Press related to the HR effect at the gene and genomic level. For example, many studies have shown that rates of synonymous evolution increase with the length of coding sequence and levels of synonymous polymorphism are lower in genes with reduced codon bias (Comeron & Aguade, 1996;Moriyama & Powell, 1996;Comeron et al, 1999). Codon usage bias also decreases as the length of coding sequence increases (Moriyama & Powell, 1998;Comeron et al, 1999;Duret & Mouchiroud, 1999).…”