A duplication including the Y allele of Lcp2 and the TRIM retrotransposon at the Lcp locus on the degenerating neo-Y chromosome of Drosophila miranda: molecular structure and mechanisms by which it may have arisen.

Evolutionary changes during the process of sex chromosome differentiation in Drosophila miranda are associated with massive DNA rearrangements. Comparing the DNA structure of the larval cuticle protein (Lcp) region from the X2 and neo-Y chromosome pair, we observed insertions, deletions and a large duplication at the neo-Y chromosomal locus. The duplication encompasses a complete copy of the neo-Y allele of Lcp2, and the ISY3 and the ISY4 insertion sequences. The latter was identified as a retrotransposon, termed TRIM. ISY3 shows DNA sequence similarity to P element homologs identified in the Drosophila obscura species group. We were interested in mechanistic aspects generating the duplication. We cannot exclude unequivocally that unequal sister-chromatid exchange could give rise to the observed duplication; however, recombination is a rare event in Drosophila males. Location and sequence of the retrotransposon TRIM served as molecular markers allowing us to reconstruct two intrachromosomal transposition events that could lead to the observed duplication.