Supplementary Information for

Tables

• Supplementary Table 1.     Coordinates of human X palindromes in hg38.
• Supplementary Table 2.     Human X-palindrome genes and gene families
• Supplementary Table 3.     Clones sequenced for this project.  Some clones contained portions of multiple palindromes.
• Supplementary Table 4.     Status of palindromes identified in SHIMS 3.0 in other chimpanzee X assemblies.
• Supplementary Table 5.     Status of palindromes identified in SHIMS 3.0 in other rhesus macaque X assemblies.
• Supplementary Table 6.     Conservation of X-palindrome gene families.
• Supplementary Table 7.     Purifying selection on X-palindrome gene families.
• Supplementary Table 8.     Rates of P17 spacer deletions in azoospermic and oligozoospermic men
• Supplementary Table 9.     Chimpanzee clones used in this project that were previously sequenced and deposited in GenBank.
• Supplementary Table 10.     PCR primers for gels shown in Supplemental Fig. 14.
• Supplementary Table 11.     Chimpanzee and rhesus macaque clones sequenced for this project and deposited in GenBank

Files

• Supplementary Note 1      Treatment of human X-palindrome genes with conflicting annotations
• Supplemental Code (zip)     

Figures

• Supplementary Figure 1      Expression of human X-palindrome gene families
• Supplementary Figure 2      Expression of human testis-biased X-palindrome gene families during spermatogenesis
• Supplementary Figure 3      Structural comparisons between palindromes in SHIMS 3.0 assemblies and existing X-Chromosome assemblies
• Supplementary Figure 4      Definition of orthologous palindromes
• Supplementary Figure 5a      Annotated square and triangular dot plots of primate X palindromes (P1, P2, P3)
• Supplementary Figure 5b      Annotated square and triangular dot plots of primate X palindromes(P4, P5, P6)
• Supplementary Figure 5c      Annotated square and triangular dot plots of primate X palindromes (P7, P8, P9)
• Supplementary Figure 5d      Annotated square and triangular dot plots of primate X palindromes (P10, P11, P12)
• Supplementary Figure 5e      Annotated square and triangular dot plots of primate X palindromes (P13, P14, P15)
• Supplementary Figure 5f      Annotated square and triangular dot plots of primate X palindromes (P16, P17, P18, P19, P20)
• Supplementary Figure 5g      Annotated square and triangular dot plots of primate X palindromes (P21, P22, P23)
• Supplementary Figure 5h      Annotated square and triangular dot plots of primate X palindromes (P24, P25, P26)
• Supplementary Figure 6      Additional examples of spacer configurations in orthologous palindromes
• Supplementary Figure 7      Expression of gene families from palindromes shared by human,chimpanzee, and macaque in chimpanzee
• Supplementary Figure 8      Expression of gene families from palindromes shared by human, chimpanzee, and macaque in macaque
• Supplementary Figure 9      Normalized coverage depths for eight palindrome spacers with at least one deletion in the 1000 Genomes dataset
• Supplementary Figure 10      Human spacer deletions with breakpoints withintandem repeats.
• Supplementary Figure 11a      Structural comparisons between human reference, human deletion,and chimpanzee for nine X palindromes with spacer deletions
• Supplementary Figure 11b      Structural comparisons between human reference, human deletion,and chimpanzee for nine X palindromes with spacer deletions
• Supplementary Figure 11c      Structural comparisons between human reference, human deletion,and chimpanzee for nine X palindromes with spacer deletions
• Supplementary Figure 12      Coverage depth for males with P17 spacer deletions
• Supplementary Figure 13      Junction for P17 spacer deletion
• Supplementary Figure 14a      Verification of human X-palindrome spacer deletions
• Supplementary Figure 14b      Verification of human X-palindrome spacer deletions