A Dual Origin of the Xist Gene minimum evolution method as implemented in the program with default parameters. MEGA Found DOC) at: doi:10.1371/journal.pone.0002521.s005 (0.04 MB Supporting Information Figure S1 Nucleotide sequences of eutherian consensus gene Xist presented in GENE BANK format. Found at: doi:10.1371/journal.pone.0002521.s001 (0.10 MB DOC) Figure S2 Alignment of the chicken proto XIC region with the human and mouse XICs. (a) Sequence alignment of part of human Xist intron 3 and a part of Lnx3 exon 3 (ACC XM_420296.1). (b) Alignment of part of human Xist intron 4 and part of Lnx3 exon 5. (c) Alignment of part of mouse Xist exon 5 and chicken Lnx3 exon 5. (d) Alignment of part of the human Xist promoter and Lnx3 exons 1 and 2. (e) Alignment of chicken Rasl11c exon 3 and the 59- region of Xist. (f) Alignment of chicken Wasf3 exon 1, 2 and the 59-region of Xist. (g) Alignment of chicken Uspl exon 1, 2 and the 59-region of Xist, (h) Alignment of chicken Uspl mRNA (ACC NM_001031123.1) and human ENOX EST BC071776. (a–g) computed with SSEARCH34 from FASTA package; (h) computed with WUBLAST 2.0. Found at: doi:10.1371/journal.pone.0002521.s002 (0.05 MB DOC) Figure S3 Homology of the mammalian consensus Xist gene exons 2, 4, 9, 10 and various transposable elements. Found at: doi:10.1371/journal.pone.0002521.s003 (0.03 MB DOC) Figure S4 Homology of consensus monomer sequences of the main blocks of tandem repeats in Xist gene and various transposable elements Found at: doi:10.1371/journal.pone.0002521.s004 (0.03 MB DOC) Figure S5 Nucleotide sequences alignment of cDNA of chicken and opossum Lnx3 genes (Mlnx3 and Clnx3) and human and bovine Xist genes. References 1. Lyon MF (1961) Gene action in the Xchromosome of the mouse (Musmusculus L.). Nature 190: 372–373. 2. Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, et al. 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Figure S6 Minimum evolution trees constructed using (a) synonymous and (b) nonsynonymous substitutions (modified Nei- Gojobori method, p-distance) [18]. The numbers for the interior branches refer to the bootstrap values with 1,000 pseudoreplicates. Found at: doi:10.1371/journal.pone.0002521.s006 (0.03 MB DOC) Table S1 Found DOC) Table S2 Found DOC) Table S3 Found DOC) Table S4 Found DOC) Table S5 Found DOC) at: doi:10.1371/journal.pone.0002521.s007 (0.04 MB at: doi:10.1371/journal.pone.0002521.s008 (0.04 MB at: doi:10.1371/journal.pone.0002521.s009 (0.03 MB at: doi:10.1371/journal.pone.0002521.s010 (0.03 MB at: doi:10.1371/journal.pone.0002521.s011 (0.06 MB Acknowledgments We would like to thank all members of the Developmental Epigenetics laboratory for helpful discussions and Claire E. Senner for valuable comments during preparation of this manuscript. Author Contributions Conceived and designed the experiments: NB SZ TN EE NK AS. Performed the experiments: EE. 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Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586–1591. PLoS ONE | www.plosone.org 10 June 2008 | Volume 3 | Issue 6 | e2521