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The genomic analysis of heterochromatin is essential for studying chromosome behavior as well as for understanding chromosome evolution. TheYchromosome ofDrosophila melanogasteris entirely heterochromatic and the under-representation of this chromosome in genomic libraries together with the difficulty of assembling its sequence has made its study very difficult. Here, we present the construction of bacterial artificial chromosome (BAC) contigs from regions h14, h16 and the centromeric region h18. The analysis of these contigs shows that telomere-derived sequences are present at internal regions. In addition, immunostaining of prometaphase chromosomes with an antibody to the kinetochore-specific protein BubR1 has revealed the presence of this protein in someYchromosome regions rich in telomere-related sequences. Collectively, our data provide further evidence for the hypothesis that theDrosophilaYchromosomes might have evolved from supernumerary chromosomes. [ABSTRACT FROM AUTHOR]