Additional file 1: Table S1. of Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki

List of BAC clones screened for FISH analysis in this study. Table S2. List of genes located on the three regions of neo-sex chromosomes in T. muenninki. Table S3. Comparison of G + C content and nucleotide substitution frequency in three regions among T. muenninki, mouse, and rat with guinea pig as outgroup. Table S4. Frequencies (%) of nucleotide substitutions in sites preceded by C or followed by G in T. muenninki neo-sex chromosomal segments and their autosomal homologs in mouse and rat. Table S5. Detection of male-specific substitutions in 24 genes located on the neo-sex chromosomes. Table S6. Male-specific substitutions observed in the pericentromeric region of the T. muenninki neo-Y chromosome. Table S7. Resulti of tests of the differences in dN/dS ratios among T. muenninki neo-X, neo-Y, and other branches. Table S8. G + C content and frequency of nucleotide substitutions in T. muenninki neo-sex chromosomes and their homologous region in mouse. Table S9. List of BAC clones identified for neo-sex sequence determination. Table S10. Results of next-generation sequencing on an Illumina HiSeq, using a 100 bp paired-end protocol and de novo assembly. Table S11. Results of next-generation sequencing on an Illumina MiSeq, using a 300 bp paired-end protocol and de novo assembly. (ZIP 110 kb)