Figure 1.
The syntenic relationship between the human X chromosome and the opossum 7, 14, and X chromosomes.
Orthologous human and opossum genes are connected by gray lines. In the human X chromosome, each stratum is indicated by a different color (stratum 1, magenta; stratum 2, yellow; stratum 3, green; and stratum 4, blue) [7]. Opossum chromosomal regions homologous with strata 1 and 2 on the human X chromosome are indicated in magenta and yellow, respectively.
Table 1.
The extent of nucleotide differences (divergences) per synonymous site values of seven gametologs in eutherians and marsupials.
Figure 2.
The phylogenetic relationships of 7 gametologs.
Neighbor-joining trees were constructed on the basis of the number of synonymous differences per site (pS). The bootstrap value supporting each internal branch is indicated at the node. Only a bootstrap value of more than 50% is shown. Sequences used for tree construction are listed in Table S1. The number of synonymous sites compared (excluding gaps) and that of operation taxonomy units (OTUs) are as follows: (A) HSFX/Y (96 sites; 13 OTUs), (B) SOX3/SRY (70 sites; 15 OTUs), (C) RBMX/Y (289 sites; 15 OTUs), (D) XKRX/Y (114 sites; 15 OTUs), (E) RPS4X/Y (289 sites; 11 OTUs), (F) SMCX/Y (1280 sites; 12 OTUs), and (G) UBE1X/Y (147 sites; 10 OTUs). Platypus sequences were used as an outgroup, except in trees B and D. For trees B and D, chicken sequences were used as an outgroup. A vertical gray bar beside each tree shows a monophyletic cluster of X- or Y-linked genes. Bold branches in E, F, and G show either marsupial- or eutherian-specific clusters. OTU names in bold indicate marsupials. The abbreviation for species names are as follows: Bota (Bos taraus), Cafa (Canis familiaris), Caja (Callithrix jacchus), Eqca (Equus caballus), Feca (Felis catus), Gaga (Gallus gallus), Hosa (Homo sapiens), Loaf (Loxodonta africana), Maeu (Macropus eugenii), Magi (Macropus giganteus), Maru (Macropus rufus), Modo (Monodelphis domestica), Mumu (Mus musculus), Orna (Ornithorhynchus anatinus), and Smma (Sminthopsis macroura). Mumu* in HSFX/Y tree (A) is located on chromosome 1 (see Discussion). BotaY sequence was not included in the UBE1X/Y tree (G) because it is truncated (Fig. S1).
Figure 3.
Window analysis of nucleotide divergence and phylogenic relationship of human SMCX/Y (A) and mouse UBE1X/Y (B) genes.
The entire genomic sequences of genes were compared in a window analysis. The window size was 500 bp, with no overlap between adjacent windows. The ordinate represents the extent of nucleotide differences and the abscissa represents position (bp). Position 1 corresponds to the beginning of exon 1 of the X-linked gene. The asterisks indicate the areas showing a statistically significant reduction in nucleotide divergence (SMCX/Y: ∼5 kb, UBE1X/Y: ∼2 kb). The unrooted tree was based on the number of synonymous differences per site. A bootstrap value of more than 50% is indicated at each node. A vertical gray bar shows a monophyletic cluster of X- or Y-linked genes. Bold branches in B show a eutherian cluster of both X- and Y-linked genes. OTU names in bold are marsupials. The abbreviations for species names are the same as those in Fig. 2. (A) The tree of the 5′ region of the gene (SMCX/Ya; exons 1–10) is shown in the left panel and that of the 3′ region (SMCX/Yb; exons 11-end) is shown in the right panel. The number of synonymous sites compared was 404 bp (SMCX/Ya) or 972 bp (SMCX/Yb) without gaps, and 11 OTUs were used. (B) The tree of the 5′ region of the gene (UBE1X/Ya; 1–1000 bp) is shown in the left panel and that of the 3′ region (UBE1X/Yb; 1001–3180 bp) is shown in the right panel. The number of synonymous sites compared was 332 bp (UBE1X/Ya) or 151 bp (UBE1X/Yb) without gaps, and 7 OTUs or 8 OTUs were used. In UBE1X/Ya, MaruY could not be included because of missing data.
Figure 4.
Schematic diagram of sex chromosome evolution in Theria.
After the divergence of Theria from monotremes, recombination was suppressed in at least 10 genes on the proto-XY chromosome in the therian ancestor; this is indicated by gray color on the chromosome. In the stem lineage of marsupials and eutherians, a gene conversion occurred in RPS4X/Y or both SMCX/Y and UBE1X/Y, respectively; this is indicated by back color on the chromosome. An asterisk means that it is not clear whether PHF6X/Y diverged at the same time as the differentiation of the other gametologs (see text).