Daniel Winston Bellott

Supplementary Information for:

Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

Daniel W Bellott, Helen Skaletsky, Tatyana Pyntikova, Elaine R Mardis, Tina Graves, Colin Kremitzki, Laura G Brown, Steve Rozen, Wesley C Warren, Richard K Wilson, David C Page

Nature 466, 612-616 (2010)

Notes:

Supplementary Note 1: (PDF)

Additional information for Supplmentary Figure 12

Figures:

Figure 1: (PDF)

The Z amplicon

Figure 2: (PDF)

Independent origin of chicken Z and human X chromosomes

Figure 3: (PDF)

Convergent gene gain on the chicken Z and human X chromosomes

Supplementary Figures and Legends 1 through 12: (PDF)

Includes:

• Supplementary Figure 1: Annotated sequence of the chicken Z chromosome
• Supplementary Figure 2: Order and orientation of Z chromosome contigs by DNA-FISH
• Supplementary Figure 3: Location of the Z chromosome centromere
• Supplementary Figure 4: Z amplicon FISH
• Supplementary Figure 5: Triangular dot plot of the Z amplicon region
• Supplementary Figure 6: Dot plots of chicken Z versus all human chromosomes
• Supplementary Figure 7: Dot plots of human X versus all chicken chromosomes
• Supplementary Figure 8: Dot plots of chicken Z and human X versus all zebrafish chromosomes
• Supplementary Figure 9: Dot plots of chicken Z and human X versus all stickleback chromosomes
• Supplementary Figure 10: Dot plots of chicken Z and human X versus all medaka chromosomes
• Supplementary Figure 11: Dot plots of chicken Z and human X versus all pufferfish chromosomes
• Supplementary Figure 12: Recombination, G+C content, and LINE density

Tables:

Supplementary Table 1: (PDF) (XLS)

Chicken Z chromosome predicted genes and human orthologs

Supplementary Table 2: (PDF) (XLS)

Chicken Z amplicon predicted genes and coordinates

Supplementary Table 3: (PDF) (XLS)

Chicken Z gene gain and loss

Supplementary Table 4: (PDF) (XLS)

Human X gene gain and loss

Supplementary Table 5: (PDF) (XLS)

BAC and fosmid clone accession numbers and position in assembly

Sequences:

chrZ_061609: (FASTA)

Fasta file of chicken Z sequence assembly (85 Mb file)

chrZ_061609_masked: (FASTA)

Fasta file of repeat-masked chicken Z sequence assembly (85 Mb file)

Supplementary Sequence File 1: (PDF) (FASTA)

Fasta file of predicted Z amplicon transcripts (as described in Supplementary Table 2)