Mácha J et al. (2012), Deep ancestry of mammalian X chromosome reveale...

XB-ART-45667

BMC Genomics 2012 Jul 16;13:315. doi: 10.1186/1471-2164-13-315.

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Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis.

Mácha J , Teichmanová R , Sater AK , Wells DE , Tlapáková T , Zimmerman LB , Krylov V .

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BACKGROUND: The X and Y sex chromosomes are conspicuous features of placental mammal genomes. Mammalian sex chromosomes arose from an ordinary pair of autosomes after the proto-Y acquired a male-determining gene and degenerated due to suppression of X-Y recombination. Analysis of earlier steps in X chromosome evolution has been hampered by the long interval between the origins of teleost and amniote lineages as well as scarcity of X chromosome orthologs in incomplete avian genome assemblies. RESULTS: This study clarifies the genesis and remodelling of the Eutherian X chromosome by using a combination of sequence analysis, meiotic map information, and cytogenetic localization to compare amniote genome organization with that of the amphibian Xenopus tropicalis. Nearly all orthologs of human X genes localize to X. tropicalis chromosomes 2 and 8, consistent with an ancestral X-conserved region and a single X-added region precursor. This finding contradicts a previous hypothesis of three evolutionary strata in this region. Homologies between human, opossum, chicken and frog chromosomes suggest a single X-added region predecessor in therian mammals, corresponding to opossum chromosomes 4 and 7. A more ancient X-added ancestral region, currently extant as a major part of chicken chromosome 1, is likely to have been present in the progenitor of synapsids and sauropsids. Analysis of X chromosome gene content emphasizes conservation of single protein coding genes and the role of tandem arrays in formation of novel genes. CONCLUSIONS: Chromosomal regions orthologous to Therian X chromosomes have been located in the genome of the frog X. tropicalis. These X chromosome ancestral components experienced a series of fusion and breakage events to give rise to avian autosomes and mammalian sex chromosomes. The early branching tetrapod X. tropicalis' simple diploid genome and robust synteny to amniotes greatly enhances studies of vertebrate chromosome evolution.

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Species referenced: Xenopus tropicalis
Genes referenced: arsd asmtl atp6ap1.2 atp7a bgn cdk16 cfp elk1 faah2 gata1 gpkow gyg2 irs4 kcnd1 mbp ophn1 otud5 pdha1 pfkfb1 piga srpx sts syn1 was

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	Fig. 1. Positions of scaffolds containing orthologs of human X chromosome genes in Xenopus tropicalis chromosomes. Of 454 amphibian orthologs of human X-borne genes identified in this study, 442 (97%) localized to X. tropicalis chromosomes 2 and 8. Mosaic distribution of X orthologs (blueâ€‰=â€‰XAR; greenâ€‰=â€‰XCR) suggests internal rearrangements after chromosomal fusions. cM â€“ centimorgans, rdc - relative distance from centromere, cen â€“ centromere.
	Fig. 2. Regions of homology between human X and Xenopus tropicalis, Gallus gallus and Monodelphis domestica chromosomes. Only gene blocks larger than 0.7 Mbp are shown. Data are from Additional file 1 and the Comparative Genomic display of the Ensembl database [18]. cen â€“ centromere, chr. - chromosome.
	Fig. 3. Regions of human chromosomes homologous to frog, chicken and opossum chromosomes. Opossum chromosomes 4 (orange) and 7 (purple) both show regions of homology on single human chromosomes 2,3, and 13, supporting their origin from a single ancestral chromosome. Amphibian (blue) and bird (grey). Figure summarizes data from Additional file 3. cen â€“ centromere.
	Fig. 4. Proposed origin of X-added region of human X chromosome. A protochromosome (blue, left), present in the progenitor of Synapsida and Sauropsida, fused with several chromosomes (pink) to form the precursor of the eutherian X-Added Region (âPre-XARâ), now extant as most of opossum chromosomes 4 and 7. The Pre-XAR subsequently fragmented and fused with the therian X-Conserved Region (XAR and opossum X, yellow) to produce the eutherian X chromosome as well as with other partners (unshaded) contributing to autosomes. Fusion partners of the proto-XAR in amphibian (green) and avian (orange) lineages are also shown.
	Additional file 2:Cytogenetic localisation of X. tropicalis genes in chromosomes. FISH-TSA localization of genes from reference scaffolds onto X. tropicalis chromosomes using scaffold-specific cDNA probes. Probes are described in Additional file 4.
	Figure 1. Positions of scaffolds containing orthologs of human X chromosome genes in Xenopus tropicalis chromosomes. Of 454 amphibian orthologs of human X-borne genes identified in this study, 442 (97%) localized to X. tropicalis chromosomes 2 and 8. Mosaic distribution of X orthologs (blueâ€‰=â€‰XAR; greenâ€‰=â€‰XCR) suggests internal rearrangements after chromosomal fusions. cM â€“ centimorgans, rdc - relative distance from centromere, cen â€“ centromere.
	Figure 2. Regions of homology between human X and Xenopus tropicalis, Gallus gallus and Monodelphis domestica chromosomes. Only gene blocks larger than 0.7 Mbp are shown. Data are from Additional file 1 and the Comparative Genomic display of the Ensembl database [18]. cen â€“ centromere, chr. - chromosome.
	Figure 3. Regions of human chromosomes homologous to frog, chicken and opossum chromosomes. Opossum chromosomes 4 (orange) and 7 (purple) both show regions of homology on single human chromosomes 2,3, and 13, supporting their origin from a single ancestral chromosome. Amphibian (blue) and bird (grey). Figure summarizes data from Additional file 3. cen â€“ centromere.
	Figure 4. Proposed origin of X-added region of human X chromosome. A protochromosome (blue, left), present in the progenitor of Synapsida and Sauropsida, fused with several chromosomes (pink) to form the precursor of the eutherian X-Added Region (âPre-XARâ), now extant as most of opossum chromosomes 4 and 7. The Pre-XAR subsequently fragmented and fused with the therian X-Conserved Region (XAR and opossum X, yellow) to produce the eutherian X chromosome as well as with other partners (unshaded) contributing to autosomes. Fusion partners of the proto-XAR in amphibian (green) and avian (orange) lineages are also shown.

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