Supplementary Information

Information for

Bellott, D.W., Skaletsky, H., Pyntikova, T., Mardis, E.R., Graves, T., Kremitzki, C.,
Brown, L.G., Rozen, S., Warren, W.C., Wilson, R.K., Page, D.C.

Convergent Evolution of Chicken Z and Human X Chromosomes by Expansion and Gene Acquisition.

All Figures and Tables are identical to those provided to the journal.
Additionally, the complete assembled sequence of the chicken Z chromosome (both raw and repeat-masked)
is available below as files chrZ_061609.fa and chrZ_061609.fa.masked.

Figures

Figure 1. Figure 1: The Z Amplicon.
Figure 2. Figure 2: Independent origin of chicken Z and human X chromosomes.
Figure 3. Figure 3: Convergent gene gain on the chicken Z and human X chromosomes.
Supplementary Figures and Legends 1-12. Supplementary Figures and Legends 1 through 12, which 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) Supplementary Table 1. Chicken Z chromosome predicted genes and human orthologs
Supplementary Table 1. (XLS) Supplementary Table 1. Chicken Z chromosome predicted genes and human orthologs
Supplementary Table 2. (PDF) Supplementary Table 2. Chicken Z amplicon predicted genes and coordinates
Supplementary Table 2. (XLS) Supplementary Table 2. Chicken Z amplicon predicted genes and coordinates
Supplementary Table 3. (PDF) Supplementary Table 3. Chicken Z gene gain and loss
Supplementary Table 3. (XLS) Supplementary Table 3. Chicken Z gene gain and loss
Supplementary Table 4. (PDF) Supplementary Table 4. Human X gene gain and loss
Supplementary Table 4. (XLS) Supplementary Table 4. Human X gene gain and loss
Supplementary Table 5. (PDF) Supplementary Table 5: BAC and fosmid clone accession numbers and position in assembly
Supplementary Table 5. (XLS) Supplementary Table 5: BAC and fosmid clone accession numbers and position in assembly

Note

Supplementary Note 1. (PDF) Additional information for Supplmentary Figure 12

Sequence Files

chrZ_061609.fa Fasta file of chicken Z sequence assembly (85 Mb file)
chrZ_061609.fa.masked Fasta file of repeat-masked chicken Z sequence assembly (85 Mb file)
Supplementary_Sequence_File_1.fa Fasta file of predicted Z amplicon transcripts (as described in Supplementary Table 2)
Supplementary_Sequence_File_1.pdf PDF version of fasta file of predicted Z amplicon transcripts (as described in Supplementary Table 2)