Supplementary Information

Supplementary Information for

Jennifer F. Hughes, Helen Skaletsky, Laura G. Brown, Tatyana Pyntikova, Tina Graves, Robert S. Fulton, Shannon Dugan,
Yan Ding, Christian J. Buhay, Colin Kremitzki, Qiaoyan Wang, Hua Shen, Michael Holder,3 Donna Villasana,
Lynne V. Nazareth, Andrew Cree, Laura Courtney, Joelle Veizer, Holland Kotkiewicz, Ting-Jan Cho, Natalia Koutseva,
Steve Rozen, Donna M. Muzny, Wesley C. Warren, Richard A. Gibbs, Richard K. Wilson & David C. Page
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

Nature (2012) http://dx.doi.org/10.1038/nature10843

Table of Contents
Figures, Tables, Notes

Figures

Figure 1 Annotated sequence of rhesus MSY

Figure 2 Extended metaphase FISH analysis of pseudoautosomal boundary

Figure 3 Extended metaphase FISH analysis of centromere

Figure 4 Extended metaphase FISH analysis to orient middle contig

Figure 5 Comparison of radiation hybrid and physical maps of rhesus MSY

Figure 6 Interphase FISH analysis of gaps

Figure 7.     Comparison of pseudoautosmal boundaries in rhesus, human and chimpanzee
        Figure 7a    Dot plot comparison of human, chimpanzee, and rhesus Y sequence to himan X sequence
        Figure 7b    Alignment of human, rhesus, and chimpanzee pseudoautosomal boundaries

Figure 8 Dot-plot comparison of rhesus and human MSYs

Figure 9 Dot-plot comparison of rhesus and chimpanzee MSYs

Figure 10 Rearrangements during evolution of rhesus, human and chimpanzee MSYs

Figure 11 Triangular dot plots of DNA sequence identities within rhesus, human and chimpanzee MSYs

Figure 12 Electronic fractionation of rhesus, human and chimpanzee MSY sequences according to intrachromosomal similarity

Figure 13 Triangular dot plot of DNA sequence identities within major rhesus ampliconic region

Figure 14 RT-PCR analysis of rhesus MSY genes

Figure 15.   Analysis of MSY ancestral pseudogenes in rhesus and human
        Figure 15a   Gpr143
        Figure 15b   Stsp
        Figure 15c   Kalp
        Figure 15d   Shroom2
        Figure 15e   Bcor
        Figure 15f   Cask

Figure 16.   Sliding-window dN/dS analyses for rhesus-human ancestral gene pairs (The legend)
        Figure 16a   Amely, CYorf15, Ddx3y
        Figure 16b   Eif1ay, Hsfy, Kdm5d, Mxra5y
        Figure 16c   Nlgn4y, Prky, Rbmy, Rps4y1
        Figure 16d   Rps4y2, Sry, Tbl1y, Tspy
        Figure 16e   Usp9y, Uty, Zfy

Figure 17 Y-linked MXRA5P/Y vs. X-linked MXRA5 dot-plot analyses in rhesus, human and chimpanzee

Figure 18.    Gene decay plots using alternative dates (The legend)
        Figure 18a
        Figure 18b

Tables

Table 1 BAC clones, GenBank accession numbers and nucleotide positions in rhesus MSY sequence assembly

Table 2 Palindromes in rhesus, human and chimpanzee MSYs

Table 3 Comparative analysis of rhesus and human MSY genes

Table 4 List of human X genes, organized by stratum, and conserved synteny in other vertebrates

Table 5 Copy numbers of genes in rhesus, human and chimpanzee

Table 6 Parameters of one-phase exponential decay models of gene numbers in MSY strata

Notes

Notes 1-5:
        Note 1. BAC selection strategy and assembly of rhesus MSY sequence
        Note 2. Determination of X-Y ancestral gene content within strata 1-5
        Note 3. Human/chimpanzee/rhesus ancestral MSY gene content
        Note 4. Discussion of dN/dS values for ancestral genes
        Note 5. Determining time of pseudogene inactivation

Sequence Files

File 1 FASTA file of rhesus MSY sequence assembly
File 2 Radiation hybrid mapping data vectors
File 3 Alignment of rhesus and human MSY sequences in FASTA format
Notes for File 3