Supplementary Information for

Tables

• Supplementary Table 1:   MSY genes and gene families demonstrated or hypothesized to
           encode proteins (expanded version)
• Supplementary Table 2:   MSY noncoding transcription units
• Supplementary Table 3:   MSY pseudogenes
• Supplementary Table 4:   MSY inverted repeats
• Supplementary Table 5:   Analysis of sequence divergence in gene-gene and
            gene-pseudogene pairs
• Supplementary Table 6:   Three euchromatic MSY sequence classes: size, G+C content,
            and interspersed repeat elements
• Supplementary Table 7:   Three euchromatic MSY sequence classes: gene and
            pseudogene content
• Supplementary Table 8: Primers for amplification of palindrome boundaries.
• Supplementary Table 9: Methods used to estimate the male-specific ages of each of the
            MSY sequences and genes, shown in Figure 8.
• Supplementary Table 10:   Six sequence species in three MSY heterochromatic regions
• Supplementary Table 11:   Chromosome Y STSs
• Additional Supplementary Table 1: Boundaries of Y chromosome inverted repeats and palindromes
• Additional Supplementary Table 2: Boundaries of amplicons in AZFc region
• Additional Supplementary Table 3: Transcribed Sequences on the Y Chromosome

Figures

• Supplementary Fig.1:       Estimating the sizes of MSY map gaps
  
• Supplementary Fig.2:       Sequence based map of the MSY (The legend)
• Supplementary Fig.3:      Chromosomal FISH analyses of selected heterochromatic landmarks
• Supplementary Fig.4:       Schematic alignment of two X-degenerate genes on Yq to their
            X chromosome homolog
• Supplementary Fig.5:       Yp evolution schematic
• Supplementary Fig.6:       Schematic alignment of the two copies of IR3
• Supplementary Fig.7:      Triangular dot-plot analyses of selected tandem repeats
• Supplementary Fig.8:       Exon/intron organization of overlapping genes
• Supplementary Fig.9:       Ks values for MSY genes and pseudogenes compared to
             their X homologs versus location on the MSY.
• Supplementary Fig.10:       Dot plot of the genomic region containing KALP and VCY
             versus the syntenic region on the X chromosome
• Supplementary Fig.11:       Closing map gaps in MSY palindrome P5
  

Sequence Files

• Supplementary File 1:      MSY sequence contig (23 Mb file) Comments
• Supplementary File 2:      NORF repeat unit consensus sequence
• Supplementary File 3:      Pseudogene sequences
• Additional Supplementary File 1:  Y chromosome landmark sequences
• Additional Supplementary File 2:  Y chromosome palindromes sequences

Notes

• Supplementary Note 1
• Supplementary Note 2
• Supplementary Note 3
• Supplementary Note 4
• Supplementary Note 5
• Supplementary Note 6
• Supplementary Note 7
• Supplementary Note 8
• Supplementary Note 9