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

Genome Research 31, 1352-1337 (2021)

Notes:

Supplementary Note 1: (PDF) (FASTA)

Treatment of human X-palindrome genes with conflicting annotations.

Figures:

Supplemental Figure S1: (PDF)

Expression of human X-palindrome gene families

Supplemental Figure S2: (PDF)

Expression of human testis-biased X-palindrome gene families during spermatogenesis

Supplemental Figure S3: (PDF)

Structural comparisons between palindromes in SHIMS 3.0 assemblies and existing X-Chromosome assemblies

Supplemental Figure S4: (PDF)

Definition of orthologous palindromes

Supplemental Figure S5a: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P1, P2, P3)

Supplemental Figure S5b: (PDF)

Annotated square and triangular dot plots of primate X palindromes(P4, P5, P6)

Supplemental Figure S5c: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P7, P8, P9)

Supplemental Figure S5d: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P10, P11, P12)

Supplemental Figure S5e: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P13, P14, P15)

Supplemental Figure S5f: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P16, P17, P18, P19, P20)

Supplemental Figure S5g: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P21, P22, P23)

Supplemental Figure S5h: (PDF)

Annotated square and triangular dot plots of primate X palindromes (P24, P25, P26)

Supplemental Figure S6: (PDF)

Additional examples of spacer configurations in orthologous palindromes

Supplemental Figure S7: (PDF)

Expression of gene families from palindromes shared by human, chimpanzee, and macaque in chimpanzee

Supplemental Figure S8: (PDF)

Expression of gene families from palindromes shared by human, chimpanzee, and macaque in macaque

Supplemental Figure S9: (PDF)

Normalized coverage depths for eight palindrome spacers with at least one deletion in the 1000 Genomes dataset

Supplemental Figure S10: (PDF)

Human spacer deletions with breakpoints within tandem repeats

Supplemental Figure S11a: (PDF)

Structural comparisons between human reference, human deletion,and chimpanzee for nine X palindromes with spacer deletions

Supplemental Figure S11b: (PDF)

Structural comparisons between human reference, human deletion,and chimpanzee for nine X palindromes with spacer deletions

Supplemental Figure S11c: (PDF)

Structural comparisons between human reference, human deletion,and chimpanzee for nine X palindromes with spacer deletions

Supplemental Figure S12: (PDF)

Coverage depth for males with P17 spacer deletions

Supplemental Figure S13: (PDF)

Junction for P17 spacer deletion

Supplemental Figure S14a: (PDF)

Verification of human X-palindrome spacer deletions

Supplemental Figure S14b: (PDF)

Verification of human X-palindrome spacer deletions

Tables:

Supplemental Table S1: (XLS)

Coordinates of human X palindromes in hg38.

Supplemental Table S2: (XLS)

Human X-palindrome genes and gene families.

Supplemental Table S3: (XLS)

Clones sequenced for this project. Some clones contained portions of multiple palindromes.

Supplemental Table S4: (XLS)

Status of palindromes identified in SHIMS 3.0 in other chimpanzee X assemblies.

Supplemental Table S5: (XLS)

Status of palindromes identified in SHIMS 3.0 in other rhesus macaque X assemblies.

Supplemental Table S6: (XLS)

Conservation of X-palindrome gene families.

Supplemental Table S7: (XLS)

Purifying selection on X-palindrome gene families.

Supplemental Table S8: (XLS)

Rates of P17 spacer deletions in azoospermic and oligozoospermic men.

Supplemental Table S9: (XLS)

Chimpanzee clones used in this project that were previously sequenced and deposited in GenBank.

Supplemental Table S10: (XLS)

PCR primers for gels shown in Supplemental Fig. 14.

Supplemental Table S11: (XLS)

Chimpanzee and rhesus macaque clones sequenced for this project and deposited in GenBank.

Files:

Supplemental Code: (FASTA) (ZIP)

Supplemental Code