Supplementary Information

Supplementary Information for

Soh, Y.Q.S., Alfoldi, J., Pyntikova, T., Brown, L.G., Graves, T., Minx, P.J., Fulton, R.S., Kremitzki, C., Koutseva, N.,
Mueller, J.L., Rosen, S., Hughes, J.F., Owens, E., Womack, J., Cao, Q., de Jong, P., Murphy, W.J., Warren, W.C.,
Wilson, R.K., Skaletsky, H., Page, D.C.

Sequencing the Mouse Y Chromosome Reveals Convergent Gene Aquisition and Amplification on Both Sex Chromosomes

Notes

Extended Experimental Procedures

Figures

Figure S1 Annotated sequence of the mouse MSY, Related to Figure 1 Figure legend
Figure S2 Structure of the mouse Y centromere, Related to Figure 2 Figure legend
Figure S3 Ampliconic sequences of the mouse Y chromosome, Related to Figure 3 Figure legend
Figure S4 Long arm ampliconic sequences in related Mus species, Related to Figure 4 Figure legend
Figure S5 Phylogenetic analysis of origins of ampliconic and multicopy genes, Related to Table 1 Figure legend
Figure S6 Dotplot analysis of Y long arm ampliconic unit versus X ampliconic units, Related to Figure 5 Figure legend
Figure S7 Evidence of recombination between long arm ampliconic units, Related to Figure 3 Figure legend

Tables

Table S1. BAC clones, GenBank accession numbers and nucleotide positions in mouse MSY sequence assembly,
Related to Experimental Procedures
Table S2. Radiation hybrid mapping data vectors, Related to Experimental Procedures
Table S3. Transcripts of the mouse Y chromosome, Related to Table 1
Table S4. Positions of long-arm amplicon Red Yellow Blue core blocks, Related to Figure 3
Table S5. BAC clones sequenced from related Mus species, Related to Experimental Procedured
Table S6. Nucleotide identity between X and Y amplified gene families, Related to Figure 5

Files

File S1. Sequence Family Variants used to identify BAC clones for sequencing, Related to Experimental Procedures
File S2. STS markers used to generate RH map, Related to Experimental Procedures
File S3. FASTA file of mouse MSY assembly, Related to Figure 1(90Mb file)
File S4. Rbmy sequences, Related to Table 1
File S5. Sly sequences, Related to Table 1
File S6. Srsy sequences, Related to Table 1
File S7. Ssty1 sequences, Related to Table 1
File S8. Ssty2 sequences, Related to Table 1
File S9. Sequence for Chr 3 transposition, Related to Figure 3
File S10. Sequence for 200kb Rbm31y insertion, Related to Figure 3
File S11. Sequences for Sly, Ssty, and Srsy identified in AKR/J, M. castaneus, M. spretus, Related to Figure 4
File S12. Slx sequences, Related to Table 1
File S13. Slxl1 sequences, Related to Table 1
File S14. Srsx sequences, Related to Table 1
File S15. Sstx sequences, Related to Table 1