Patterns of Base Composition Within the Genes of Drosophila melanogaster

Abstract. Base composition is not uniform across the genome of Drosophila melanogaster. Earlier analyses have suggested that there is variation in composition in D. melanogaster on both a large scale and a much smaller, within-gene, scale. Here we present analyses on 117 genes which have reliable intron/exon boundaries and no known alternative splicing. We detect significant heterogeneity in G+C content among intron segments from the same gene, as well as a significant positive correlation between the intron and the third codon posi-tion G+C content within genes. Both of these observa-tions appear to be due, in part, to an overall decline in intron and third codon position G+C content along Dro-sophila genes with introns. However, there is also evi-dence of an increase in third codon position G+C content at the start of genes; this is particularly evident in genes without introns. This is consistent with selection acting against preferred codons at the start of genes. Key words: G+C content — Isochores — Synony-mous codon us