Daniel Winston Bellott

Supplementary Information for:

Large palindromes on the primate X Chromosome are preserved by natural selection

Emily K Jackson, Daniel W Bellott, Ting-Jan Cho, Helen Skaletsky, Jennifer F Hughes, Tatyana Pyntikova, David C Page

bioRxiv (2020)

Files:

Supplemental Materials: (PDF)

Includes:

• Supplemental Note 1: Treatment of human X-palindrome genes with conflicting annotations
• Supplemental Figure 1: Expression of human X-palindrome gene families
• Supplemental Figure 2: Expression of human testis-biased X-palindrome gene families during spermatogenesis
• Supplemental Figure 3: Structural comparisons between palindromes in SHIMS 3.0 assemblies and existing X-Chromosome assemblies
• Supplemental Figure 4: Definition of orthologous palindromes
• Supplemental Figure 5: Annotated square and triangular dot plots of primate X palindromes
• Supplemental Figure 6: Additional examples of spacer configurations in orthologous palindromes
• Supplemental Figure 7: Expression of gene families from palindromes shared by human, chimpanzee, and macaque in chimpanzee
• Supplemental Figure 8: Expression of gene families from palindromes shared by human, chimpanzee, and macaque in macaque
• Supplemental Figure 9: Normalized coverage depths for eight palindrome spacers with at least one deletion in the 1000 Genomes dataset
• Supplemental Figure 10: Human spacer deletions with breakpoints within tandem repeats
• Supplemental Figure 11: Structural comparisons between human reference, human deletion, and chimpanzee for nine X palindromes with spacer deletions
• Supplemental Figure 12: Coverage depth for males with P17 spacer deletions
• Supplemental Figure 13: Junction for P17 spacer deletion
• Supplemental Figure 14: Verification of human X-palindrome spacer deletions
• Supplemental Table 1: Coordinates of human X palindromes in hg38
• Supplemental Table 2: Clones sequenced for this project
• Supplemental Table 3: Status of palindromes identified in SHIMS 3.0 in other chimpanzee X assemblies
• Supplemental Table 4: Status of palindromes identified in SHIMS 3.0 in other rhesus macaque X assemblies
• Supplemental Table 5: Conservation of X-palindrome gene families
• Supplemental Table 6: Purifying selection on X-palindrome genes
• Supplemental Table 7: Chimpanzee clones used in this project that were previously sequenced and deposited in GenBank
• Supplemental Table 8: Rates of P17 spacer deletions in azoospermic and oligozoospermic men
• Supplemental Table 9: PCR primers for gels shown in Supplemental Figure 14
• Supplemental Table 10: Chimpanzee and rhesus macaque clones sequenced for this project and deposited in GenBank