Supplemental Materials
Supplemental Figure 1. Positions of five sex-linked BACs and the structure of six sexlinked genes. A. The position of BACs in the MSY region of papaya. B. The position and
orientation of Genes 1-3. The line represented the BAC and the box with arrow represented
the gene and its orientation. The shaded areas connected corresponding genes. Gene3 had not
been found in Y nor Yh chromosome. C. The position and orientation of Genes 4-6. Only Cterminal of Gene4 was found in the Y BAC (DM62K05). D. The structure of Genes 1-6. The
length of the gene was shown in proportion. The orange bar represented exons and the blue
line the introns. The amplified genomic sequences were indicated as blue circle.
Supplemental Figure 2. Maximum likelihood phylogenetic trees of sex-linked Genes1 to 6
and autosomal ANKYRIN among Carica and Vasconcellea species.
Supplemental Figure 3. Maximum parsimony phylogenetic trees of sex-linked Genes1 to 6
and autosomal ANKYRIN among Carica and Vasconcellea species.
Supplemental Figure 4. Neighbor-joining phylogenetic trees of sex-linked Genes1 to 6 and
autosomal ANKYRIN among Carica and Vasconcellea species.
Supplemental Figure 5. Single nucleotide polymorphisms (SNPs) in coding sequences of
Genes 1-6 and autosomal gene ANKYRIN. The alignment was first done with DNA
sequences. Once a mutation was found, the corresponding codon was translated into amino
acid residue to examine whether it was a synonymous or nonsynonymous mutation. The
corresponding color showed the resultant amino acid translation from DNA to protein.
Supplemental Figure 6. Bayesian phylogenetic trees of sex-linked Genes1 to 6 and
autosomal ANKYRIN among Carica and Vasconcellea species after removing the sequences
that showed gene conversion.
Supplemental Tables
Supplemental Table 1. List of degenerate primers used to amplify the target genes.
Supplemental Table 2. List of Vasconcellea specific primers used to amplify the target
genes and conduct primer walking for sequencing the amplified fragments.
Supplemental Table 3. Annotation of six sex-linked genes and autosomal gene ankyrin.
Supplemental Table 4. Estimates of synonymous and nonsynonymous nucleotide
divergence within and between species of Gene 2
Supplemental Table 5. Estimates of synonymous and nonsynonymous nucleotide
divergence within and between species of Gene 3
Supplemental Table 6. Estimates of synonymous and nonsynonymous nucleotide
divergence within and between species of Gene 4
Supplemental Table 7. Estimates of synonymous and nonsynonymous nucleotide
divergence within and between species of Gene 5
Supplemental Table 8. Estimates of synonymous and nonsynonymous nucleotide
divergence within and between species of Gene 6
Supplemental Table 9. Fragments with possible gene conversion detected by GENECOV.
The conversion within species were highlighted.
Supplemental Note: Perl script for SNPs analysis