A Drosophila heat shock locus with a rapidly diverging sequence but a conserved structure

Cytological studies have shown that the heat shock loci 93D of Drosophila melanogaster and 2-48B of Drosophila hydei have several characteristics which suggest that they are homologous loci, yet sequence homology is barely detectable by cross-hybridization. Using cloned DNA sequences we have compared the two loci. Both loci produce transcripts of similar size and number. We have characterized the three predominant transcripts. In each species all three transcripts start at or about the same place within the unique portion of the gene. The longest transcript (approximately 9-10 kilobases) continues through several kilobases of short tandem repeats. The two shorter (1.9 and 1.2 kilobases) transcripts terminate 5' to the repeats. The repeat sequences are strongly conserved within a species but between species they have diverged both in length and in sequence. The longest homology is 9 nucleotides. The unique portions have also diverged significantly but do have some regions of conserved sequence. In both species the cytoplasmic transcript is spliced and polyadenylated but does not appear to contain a significant open reading frame. Thus, although the sequence of this locus has diverged significantly there are conserved features which suggest that the function of the locus is also conserved.