FIGURE 1. Repetitive structure of euchromatic NRY.

Bottom, schematic of the Y chromosome, comprising large NRY flanked by pseudoautosomal regions (yellow). NRY is divided into euchromatic and heterochromatic (tan, shown truncated) portions, roughly 24 and 30 Mb, respectively. pter, short-arm telomere; cen, centromere; qter, long-arm telomere. Within euchromatic NRY, regions rich in NRY-specific amplicons (blue) or sequence similarity to X chromosome (red) are shown. Above chromosome schematic are positions of some NRY genes; most are found in amplicons (blue) or have X-linked homologues (red). Above genes is a plot of the average number of NRY BACs that contain each of the 758 STSs mapped (136 of these STSs at two or more locations) along euchromatic NRY. As expected, STSs in amplicon regions tended to be present in more BACs than STSs in X-homologous or unshaded regions. (Plotted values are local averages within sliding window of five consecutive STSs; values reflect all NRY BACs containing those STSs, not just BACs assigned to site indicated.) Some amplicon regions were under-represented in the BAC library; four gaps remain (red diamonds; 100 kb each) in BAC coverage of NRY. Top, STS-based dot plot of euchromatic NRY. Each dot reflects occurrence of a particular STS at two points in map (complete map shown in Fig. 1 in Supplementary Information). Dots fall almost exclusively within amplicon regions. Many repeats of entire groups of STSs are apparent, with lines parallel to light grey diagonal indicating direct repeats and lines perpendicular to light grey diagonal indicating inverted repeats. Green arrows, inverted repeats flanking 3.5-Mb inversion (see text). Pale red lines, centromere.