Supplementary Information for

Tables

• Supplementary Table S1:   BAC clone locations and accessions
  
• Supplementary Table S2:   Sequence classes of the SHR/Akr Y chromosome
  
• Supplementary Table S3:   Rat Y transcript locations
  
• Supplementary Table S4:   X-Y pair identity
  
• Supplementary Table S5:   Accessions used for gene expression analyses
  
• Supplementary Table S6:   Accessions used for copy number analyses
  

Figures

• Supplementary Fig.S1:       Annotated sequence of SHR/Akr rat Y (The legend)
  
• Supplementary Fig.S2:       Fluoresence in situ hybridization mapping of the rat sex chromosomes.
  
• Supplementary Fig.S3:       Hi-C mapping of the rat Y chromosome
  
• Supplementary Fig.S4:       Dot plot comparing rat and mouse Y chromosomes
  
• Supplementary Fig.S5:       Maximum-likelihood tree of Ssty family members in rat
  
• Supplementary Fig.S6:       Additional meiotic spreads showing location of X-transposed region BAC clones
  

Supplementary Data

• Data S1:      Fasta sequence of the SHR/AKR Rat Y chromosome assembly
  
• Data S2:      AGP file describing the SHR/AKR Rat Y chromosome assembly
  
• Data S3:      Rat Y transcript sequences
  
• Data S4:      Transcribed sequences from the rat Y and Xq XTR, gff file
  
• Data S5:      X/Y gene alignments
  
• Data S6:      Fasta sequence of the SHR/AKR Rat Xp assembly
  
• Data S7:      Fasta sequence of the SHR/AKR Rat Xq assembly
  
• Data S8:      Fasta alignment of Xp and Yq PAR sequences
  
• Data S9:      Fasta alignment of Xq and Yp XTR sequences, distal segment
  
• Data S10:    Fasta alignment of Xq and Yp XTR sequences, proximal segment
  
• Data S11:    Fasta sequence of long read sequence contigs and redundant BACs