The extent of nucleotide differences (divergences) per synonymous site values of seven gametologs in eutherians and marsupials.

*1<p>: In humans, the following genes possess multiple copies (number of copies); <i>HSFX</i> (2), <i>HSFY</i> (2), <i>RBMY</i> (7), <i>XKRY</i> (8), and <i>RPS4Y</i> (2). For genes with multiple copies, the average value was taken over all X-Y pairs.</p>*2<p>: Differences were calculated using a modified version of the Nei-Gojobori method. Values in parentheses were <i>K_S</i> estimated with corrections by the Jukes-Cantor Method. The standard error (values after “±”) was calculated from the maximum variance <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045488#pone.0045488-Takahata2" target="_blank">[53]</a> and by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045488#pone.0045488-Kimura2" target="_blank">[54]</a>.</p>*3<p>: Previous stratum was defined by previous studies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045488#pone.0045488-Lahn1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045488#pone.0045488-Skaletsky1" target="_blank">[18]</a>.</p>*4<p>: For other sequences, nucleotide differences and divergences in marsupial <i>UBE1X/Y</i> and <i>UBE1X/Yb</i> are calculated from a comparison of opossum X with kangaroo Y. However, those in marsupial <i>UBE1X/Ya</i> could not be calculated because the corresponding nucleotide sequence of kangaroo is not available. Values for <i>RSMBX/Y</i>, <i>SOX3/SRY</i>, and <i>HSFX/Y</i> are gametologs in wallaby, those in dunnart, and opossum X and kangaroo Y, respectively.</p

No Evidence for a Second Evolutionary Stratum during the Early Evolution of Mammalian Sex Chromosomes

<div><p>Mammalian sex chromosomes originated from a pair of autosomes, and homologous genes on the sex chromosomes (gametologs) differentiated through recombination arrest between the chromosomes. It was hypothesized that this differentiation in eutherians took place in a stepwise fashion and left a footprint on the X chromosome termed “evolutionary strata.” The evolutionary stratum hypothesis claims that strata 1 and 2 (which correspond to the first two steps of chromosomal differentiation) were generated in the stem lineage of Theria or before the divergence between eutherians and marsupials. However, this prediction relied solely on the molecular clock hypothesis between pairs of human gametologs, and molecular evolution of marsupial sex chromosomal genes has not yet been investigated. In this study, we analyzed the following 7 pairs of marsupial gametologs, together with their eutherian orthologs that reside in stratum 1 or 2: <em>SOX3/SRY</em>, <em>RBMX/Y</em>, <em>RPS4X/Y</em>, <em>HSFX/Y</em>, <em>XKRX/Y</em>, <em>SMCX/Y</em> (<em>KDM5C/D</em>, <em>JARID1C/D</em>), and <em>UBE1X/Y</em> (<em>UBA1/UBA1Y</em>). Phylogenetic analyses and estimated divergence time of these gametologs reveal that they all differentiated at the same time in the therian ancestor. We have also provided strong evidence for gene conversion that occurred in the 3′ region of the eutherian stratum 2 genes (<em>SMCX/Y</em> and <em>UBE1X/Y</em>). The results of the present study show that (1) there is no compelling evidence for the second stratum in the stem lineage of Theria; (2) gene conversion, which may have occurred between <em>SMCX/Y</em> and <em>UBE1X/Y</em> in the eutherian lineage, potentially accounts for their apparently lower degree of overall divergence.</p> </div

Schematic diagram of sex chromosome evolution in Theria.

<p>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 <i>RPS4X/Y</i> or both <i>SMCX/Y</i> and <i>UBE1X/Y</i>, respectively; this is indicated by back color on the chromosome. An asterisk means that it is not clear whether <i>PHF6X/Y</i> diverged at the same time as the differentiation of the other gametologs (see text).</p

The syntenic relationship between the human X chromosome and the opossum 7, 14, and X chromosomes.

<p>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) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045488#pone.0045488-Lahn1" target="_blank">[7]</a>. Opossum chromosomal regions homologous with strata 1 and 2 on the human X chromosome are indicated in magenta and yellow, respectively.</p

Additional file 1: Table S1. of The evolutionary process of mammalian sex determination genes focusing on marsupial SRYs

The functionally important amino acid residues and substitutions in SRY. Table S2. The pair of proteins and DNA used for the molecular dynamics analysis. Table S3. The list of amino acid residues interacting with DNA. Table S4. The values of the binding energy of protein and DNA. (XLSX 17 kb

<i>In Vivo</i> Function and Evolution of the Eutherian-Specific Pluripotency Marker UTF1

<div><p>Embryogenesis in placental mammals is sustained by exquisite interplay between the embryo proper and placenta. <i>UTF1</i> is a developmentally regulated gene expressed in both cell lineages. Here, we analyzed the consequence of loss of the <i>UTF1</i> gene during mouse development. We found that homozygous <i>UTF1</i> mutant newborn mice were significantly smaller than wild-type or heterozygous mutant mice, suggesting that placental insufficiency caused by the loss of <i>UTF1</i> expression in extra-embryonic ectodermal cells at least in part contributed to this phenotype. We also found that the effects of loss of <i>UTF1</i> expression in embryonic stem cells on their pluripotency were very subtle. Genome structure and sequence comparisons revealed that the <i>UTF1</i> gene exists only in placental mammals. Our analyses of a family of genes with homology to UTF1 revealed a possible mechanism by which placental mammals have evolved the <i>UTF1</i> genes.</p></div

Isolation of UTF1 homozygous mutant ESCs from blastocysts.

<p>(A) Western blot analyses of pluripotency marker proteins in ESCs generated by outgrowth of <i>UTF1</i> homozygous and heterozygous mutant blastocysts. (B) Comparison of the differentiation propensity between <i>UTF1</i> homozygous and heterozygous mutant ESCs. <i>UTF1</i> homozygous and heterozygous mutant ESCs were induced to differentiate by embryoid body formation. RNAs were prepared at the indicated days. cDNAs generated by reverse transcription were used to examine the levels of differentiation marker gene expression by real-time PCR. Data represent the mean with SD (n = 3). (C) Western blot analyses of Arf tumor suppressor protein in <i>UTF1</i> heterozygous and homozygous mutant ESCs. (D) Chimeric mouse analyses of <i>UTF1</i> homozygous mutant ESCs. Fluorescent Kusabira orange-labeled <i>UTF1</i> homozygous mutant ESCs generated from a blastocyst were injected into blastocysts. Embryos were allowed to develop in a recipient female mouse. Left and right panels are bright-field and fluorescence images of a 9.5 dpc embryo recovered from the recipient mouse, respectively.</p

Acquisition of pluripotency by <i>UTF1</i>-knockout homozygotes.

<p>(A) Comparison of the frequency between knockouts of first and second alleles in serial <i>UTF1</i> gene targeting. A <i>UTF1-</i>targeting vector carrying the puromycin resistance gene was introduced into wild-type and <i>UTF1</i> heterozygous mutant ESCs bearing the blasticidin resistance gene in one of the <i>UTF1</i> loci by electroporation, and were then selected with medium containing puromycin only or puromycin and blasticidin, respectively. Genomic DNAs were prepared from drug-resistant clones and used as templates for PCR to distinguish between homologous recombination and random integration of the vector. Frequencies of targeted disruption in wild-type and <i>UTF1</i> heterozygous mutant ESCs were 2.08% and 0.88%, respectively. Because the probability of targeted disruption in wild-type ESCs is considered to be twice as high as that in heterozygous mutant ESCs, we concluded that the second allele knockout in serial gene targeting of the <i>UTF1</i> loci is not a rare event compared with the first allele knockout. (B) Western blot analyses of UTF1 and other pluripotency marker proteins in <i>UTF1</i> homozygous mutant ESCs (UTF1 KO ES) generated in A and iPSCs generated from <i>UTF1</i> homozygous mutant MEFs (UTF1 KO iPS). Wild-type ESCs were used as references. (C) H&E-staining of sections of a teratoma containing differentiated cells of all three germ layers generated by injection of <i>UTF1</i>-null iPSCs into nude mice. Representative portions of the three germ layers are marked by brackets.</p

Implication of derivation of <i>UTF1</i> from <i>ZCSAN20-like</i> in an ancestor of placental mammals.

<p>(A) Diagram showing the domain structure of ZCSAN20-like protein with the amino acid sequence (1–867). Triangles with numbers indicate positions corresponding to exon-intron boundaries of the gene encoding ZCSAN20-like protein. Brown and black bars indicate positions with significant similarity to UTF1, which are shown in B and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068119#pone.0068119.s006" target="_blank">Figure S6</a>, respectively. (B) Alignment of the amino acid sequence of the SANT domain of human UTF1 with that of ZSCAN20-like protein. Amino acid identity and similarity between UTF1 and ZSCAN20-like are marked by double and single dots, respectively. (C) A neighbor-joining tree analysis was constructed based on the number of nucleotide differences per site. The bootstrap value supporting each internal branch is indicated at the node. A cluster containing UTF1s and opossum ZSCAN20-like is boxed with a red line. (D) Model of <i>UTF1</i> evolution in a common ancestor of eutherian (placental) mammals after divergence which separates from marsupials. Data in B, C, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068119#pone.0068119.s006" target="_blank">Figure S6</a> suggest that the <i>UTF1</i> gene was derived from a portion of the <i>ZCAN20-like</i> gene. After this transition, extensive nucleotide sequence changes occurred to evolve the <i>UTF1</i> gene, which eliminated the trace of homology between UTF1 and ZSCAN20-like except for two regions including their SANT domains. However, the depicted panel is just one possibility. For example, regions without similarity to the <i>ZCAN20-like</i> gene (depicted with a red rectangle) could have arisen <i>de novo</i> by modification of the sequences that had been present before translocation of the <i>ZCAN20-like</i> gene. The second SANT domain of ZSCAN20-like and its possible derivative in UTF1 are indicated by a brown bold line, while regions corresponding to those shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068119#pone.0068119.s006" target="_blank">Figure S6</a> are marked by a black line.</p

Role of UTF1 in the placenta.

<p>(A) Immunohistochemical analyses of UTF1 protein expression in wild-type placentas at 12.5 and 14.5 dpc. LB, labyrinth layer. (B) H&E-stained sections of <i>UTF1</i> heterozygous and homozygous mutant placentas. The boundary between the LB region and others is indicated by the dotted line. Each column of bar graph represents the mean of placenta weight with standard deviation (SD) (n = 3). *, p<0.05; **, p<0.01. (C) Cells in the mitotic phase in <i>UTF1</i> homozygous and heterozygous mutant placentas at 12.5 dpc visualized by immunostaining with an anti-phospho-histone H3 (Ser10) antibody. Phospho-histone H3-positive mitotic cells are marked by white arrowheads. Cells were counterstained with 4′,6′ diamidino-2-phenylindole (DAPI). Each column of bar graph represents the mean of number of phosphorylated histone H3 in 0.1 mm square with SD (n = 3). *, p<0.05. (D) Magnified view of H&E-stained sections of placentas. Placentas with the indicated genotypes were sectioned and stained. Dc, deciduas; Gly, glycogen trophoblast; TGC, trophoblast giant cell; Sp, spongiotrophoblast.</p