Supplementary Information for

Tables

• Supplementary Table 1    Reassembling the human X chromosome: 33 regions scrutinized, 29 of which we sequenced using the SHIMS approach.
• Supplementary Table 2    Genes shared between human and mouse X chromosomes.
• Supplementary Table 3    Human X-linked genes with no detectable ortholog on the mouse X chromosome.
• Supplementary Table 4    Mouse X-linked genes with no detectable ortholog on the human X chromosome
• Supplementary Table 5    Tallies of X-linked gene classifications depicted graphically in Figure 5.
• Supplementary Table 6    Tissue expression of X-linked genes shared between human and mouse.
• Supplementary Table 7    Expression patterns of independently acquired human X-linked genes.
• Supplementary Table 8    Expression patterns of independently acquired mouse X-linked genes.
• Supplementary Table 9    Documenting expression of individual members of independently acquired X-linked multicopy and ampliconic gene families in human and mouse.
• Supplementary Table 10    Expression patterns of all human autosomal genes.
• Supplementary Table 11    Expression patterns of all mouse autosomal genes.
• Supplementary Table 12    All OMIM X-linked phenotypes where the molecular basis is known.
• Supplementary Table 13    Expression patterns between the sexes, in the heart and kidney, of human genes that follow Ohno's law.
• Supplementary Table 14    Expression patterns between the sexes, in the heart and kidney, of mouse genes that follow Ohno's law.

Figures

• Figure S1     Triangular dot-plots of a revised human X-ampliconic region containing the CT45 gene family. a, The previous multi-haplotype reference sequence. Each dot represents 100% nucleotide identity within a window of 100 nucleotides; direct repeats appear as horizontal lines, inverted repeats as vertical lines, and palindromes as vertical lines that nearly intersect the baseline. Black arrows immediately below plots denote positions and orientations of amplicons. Further below, sequenced clones from RP-11, WI-2, RP-13 libraries (each from a different individual) contributing to the assembly are depicted as green, red, and orange bars, respectively; each bar reflects the extent and position within the assembly of finished sequence for that clone. (As per the human genome assembly standard, finished-sequence overlaps between adjoining clones are limited to 2 kb.) Genbank accession numbers are in Supplementary Table 1. b, SHIMS assembly of same region. All BACs derive from RP-11 library (one male) and are fully sequenced; each BAC's finished sequence extensively overlaps those of adjoining BACs.
• Figure S2     Triangular dot-plots of a revised human X-ampliconic region containing the PNMA6 gene family.a, The previous multi-haplotype reference sequence. Each dot represents 100% nucleotide identity within a window of 100 nucleotides; direct repeats appear as horizontal lines, inverted repeats as vertical lines, and palindromes as vertical lines that nearly intersect the baseline; gaps are indicated by gray shading. Black arrows immediately below plots denote positions and orientations of amplicons. Further below, sequenced clones from RP-1 and RP-11 libraries (each from a different individual) contributing to the assembly are depicted as orange and green bars, respectively; each bar reflects the extent and position within the assembly of finished sequence for that clone. (As per the human genome assembly standard, finished-sequence overlaps between adjoining clones are limited to 2 kb.) Genbank accession numbers are in Supplementary Table 1. b, SHIMS assembly of same region. All clones derive from ABC-8 library (one male) and are fully sequenced and in blue; each clone’s finished sequence extensively overlaps those of adjoining clones.
• Figure S3     Triangular dot-plots, based on SHIMS assemblies, of newly identified palindromic amplicons. a, An ampliconic region within chromosomal interval Xq28. Each dot represents 100% nucleotide identity within a window of 100 nucleotides. Direct repeats appear as horizontal lines, inverted repeats as vertical lines, and palindromes as vertical lines that nearly intersect the baseline; gaps are indicated by gray shading. Black arrows immediately below plots denote positions and orientations of amplicons. Newly identified amplicons are indicated with asterisks. Further below, sequenced clones from the CH-17 (haploid genome) library contributing to the assembly are depicted as red bars. Genbank accession numbers are in Supplementary Table 1. b, An ampliconic region within chromosomal interval Xp21.1. Each dot represents 100% nucleotide identity within a window of 50 nucleotides. Sequenced clones from the RP-11 (one male) library contributing to the assembly are depicted as green bars.
• Figure S4     Percentage of genes expressed predominantly in the ovary. The horizontal dotted line represents the proportion of genes on all autosomes exhibiting ovary-predominant expression. SC = single copy, MC = multicopy, AMP = ampliconic. The frequencies of shared MC, shared AMP, and independently acquired SC, MC, AMP genes are not statistically different (P-value =0.05) from either autosomal or X-linked single-copy gene frequencies (Chi-square test, with Yates’ correction).
• Figure S5     Dot plots of human X chromosome versus six different mammalian X chromosomes. Dot plots were performed using BLASTZ nucleotide alignments, where each dot represents a high scoring stretch of nucleotide sequence with more than 70% identity (see methods). Chimpanzee, rhesus, dog, horse and cow X chromosome whole genome shotgun assemblies are comprised almost exclusively of single-copy sequence (Table 1), making it unclear if human and mouse X-ampliconic sequences are conserved in these species. We can see that the human X chromosome single-copy sequence is shared with other mammals, but it is unclear whether its amplicons are until SHIMS-based sequence is generated for the chimpanzee, rhesus, dog, horse, and cow X chromosomes. The phylogenetic tree is based upon a recent comparison of 29 mammalian genomes (Lindblad-Toh K. et al. 2011). Reference:Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476-82 (2011).
• Figure S6     Hybrid male-sterility loci in mice that map to the X chromosome. Based upon the mouse genome informatics phenotype database, three loci (Mhstq2, Ihtw1, Hstx1) are X-linked and map within or adjacent to independently acquired genes. Mhstq2 (male hybrid sterility QTL 2; Elliott et al., 2004) is genetically linked to chromosomal position 29.5 Mb -- within the Slx amplicon -- and is associated with low sperm production in hybrids. Ihtw1 (interspecific hybrid testis weight 1; Elliott et al., 2001) is genetically linked to chromosomal position 50.3 Mb (the map position of the DXMit23 marker) -- 500 kb proximal to the Slx-like-1 amplicon -- and is associated with reduced levels of male fertility and reduced testis weight in hybrids. Hstx1 (hybrid sterility, X chromosome 1; Storchova et al., 2004) is genetically linked to chromosomal position 69.5 Mb (the map position of the DXMit119 marker) -- flanked by the 4930567H17Rik-amplicon (67.6 Mb) and the Xlr-amplicon (70.5 Mb) -- and is associated with reduced levels of male fertility, reduced testis weight, reduced sperm count and increased abnormal sperm head morphology in hybrids. A fourth locus, Hst3, maps to the X chromosome pseudoautosomal region (par) and is considered to be due to differences in the PAR between Mus spretus and Mus musculus. The only other known hybrid sterility loci in the mouse genome map to chromosome 17. Of the six loci that map to chromosome 17, five loci (Hst4, Hst5, Hst6, Hst7, and Mhstq1) all map within close linkage at the proximal end of chromosome 17, near the t-complex, and the remaining locus (Hst1) maps to Prdm9.

Notes