Comparative genomic hybridization (CGH) was used to identify and probe sex
chromosomes in several XY and WZ systems. Chromosomes were hybridized simul
taneously with FluorX-labelled DNA of females and Cy3-labelled DNA of males
in the presence of an excess of Cot-l DNA or unlabelled DNA of the homogam
etic sex. CGH visualized the molecular differentiation of the X and Y in th
e house mouse, Mus musculus, and in Drosophila melanogaster: while autosome
s were stained equally by both probes, the X and Y chromosomes were stained
preferentially by the female-derived or the male-derived probe, respective
ly. There was no differential staining of the X and Y chromosomes in the fl
y Megaselia scalaris, indicating an early stage of sex chromosome different
iation in this species. In the human and the house mouse, labelled DNA of m
ales in the presence of unlabelled DNA of females was sufficient to highlig
ht Y chromosomes in mitosis and interphase. In WZ sex chromosome systems, t
he silkworm Bombyx mori, the flour moth Ephestia kuehniella, and the wax mo
th Galleria mellonella, the W chromosomes were identified by CGH in mitosis
and meiosis. They were conspicuously stained by both female- and male-deri
ved probes, unlike the Z chromosomes, which were preferentially stained by
the male-derived probe in E. kuehniella only but were otherwise inconspicuo
us. The ratio of female:male staining and the pattern of staining along the
W chromosomes was species specific. CGH shows that W chromosomes in these
species are molecularly well differentiated from the Z chromosomes. The con
spicuous binding of the male-derived probe to the W chromosomes is presumab
ly due to an accumulation of common interspersed repetitive sequences.