DOI: 10.1101/gr.9.5.437. Genomic Structure and Comparative Analysis of Nine <i>Fugu</i> Genes: Conservation of Synteny with Human Chromosome Xp22.2

Genomic Structure and Comparative Analysis of Nine Fugu Genes: Conservation of Synteny with Human Chromosome Xp22.2–p22.1

10.1101/gr.9.5.437

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

Abstract

The pufferfish Fugu rubripes has a compact 400-Mb genome that is ∼7.5 times smaller than the human genome but contains a similar number of genes. Focusing on the distal short arm of the human X chromosome, we have studied the evolutionary conservation of gene orders in Fugu and man. Sequencing of 68 kb of Fugugenomic DNA identified nine genes in the following order: (SCML2)-STK9, XLRS1, PPEF-1, KELCH2, KELCH1, PHKA2, AP19, and U2AF1-RS2. Apart from an evolutionary inversion separatingAP19 and U2AF1-RS2 from PHKA2, gene orders are identical in Fugu and man, and all nine human homologs map to the Xp22 band. All Fugu genes were found to be smaller than their human counterparts, but gene structures were mostly identical. These data suggest that genomic sequencing in Fugu is a powerful and economical strategy to predict gene orders in the human genome and to elucidate the structure of human genes.[Sequence data for this article were deposited with the EMBL/GenBank data libraries under accession nos. AJ011381 and AF094327.]

Bibliography

Brunner, B., Todt, T., Lenzner, S., Stout, K., Schulz, U., Ropers, H.-H., & Kalscheuer, V. M. (1999). Genomic Structure and Comparative Analysis of Nine Fugu Genes: Conservation of Synteny with Human Chromosome Xp22.2âp22.1. Genome Research, 9(5), 437â448.

Authors 7

Bodo Brunner (first)
Tilman Todt (additional)
Steffen Lenzner (additional)
Karen Stout (additional)
Ute Schulz (additional)
Hans-Hilger Ropers (additional)
Vera M. Kalscheuer (additional)

References 39 Referenced 31

10.1038/387140a0 / Nature / How good a model is the Fugu genome. by Aparicio (1997)
10.1101/gr.7.12.1138 / Genome Res. / The comparative genomic structure and sequence of the surfeit gene homologs in the puffer fish Fugu rubripes and their association with CpG-rich islands. by Armes (1997)
10.1038/ng0595-67
10.1093/nar/24.14.2730
10.1016/0022-2836(94)90056-6
10.1073/pnas.89.6.2002
10.1038/366265a0 / Nature / Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. by Brenner (1993)
10.1093/hmg/5.5.653
10.1073/pnas.89.6.2096
10.1006/geno.1995.1075
10.1038/387140b0 / Nature / How good a model is the Fugu genome. by Elgar (1997)
Felsenstein J. (1981) The statistical approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. in Cladistics: Perspectives on the reconstruction of evolutionary history; workshop on the theory and application of cladistic methodology, eds Duncan T. Stues T.F. (Columbia University Press, New York, NY), pp 22–28.
———. Confidence limits on phylogenies an approach using the bootstrap. Evolution 39: 783–791.. (10.1111/j.1558-5646.1985.tb00420.x)
10.1038/385305a0
10.1096/fasebj.9.8.7768349 / FASEB J. / The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification. by Hanks (1995)
10.1093/hmg/4.1.77 / Hum. Mol. Genet. / Mutations in the phosphorylase kinase gene PHKA2 are responsible for X-linked liver glycogen storage disease. by Hendrickx (1995)
10.1101/gr.6.12.1185
10.1016/S0097-8485(96)80013-1
10.1038/ng0993-74
10.1016/S0021-9258(18)99141-6 / J. Biol. Chem. / AP17 and AP19 the mammalian small chains of the clathrin-associated protein complexes show homology to YAP17P their putative homolog in yeast. by Kirchhausen (1991)
10.1006/geno.1995.9879
10.1016/0888-7543(95)80044-M
10.1016/0888-7543(95)80179-P
10.1073/pnas.95.22.13068
10.1093/hmg/6.7.1137
10.1006/geno.1998.5391
10.1093/protein/10.1.1
10.1083/jcb.138.4.799
10.1038/ng1097-164
10.1006/geno.1997.4913
10.1093/nar/15.17.7155
10.1073/pnas.94.21.11639
10.1016/0896-6273(90)90141-2
10.1016/0092-8674(92)90230-A
10.1073/pnas.93.4.1366
10.1006/geno.1998.5224
10.1101/gad.9.9.1074
10.1073/pnas.94.23.12462
10.1016/S0378-1119(97)00423-X

Dates

Type	When
Created	3 years, 9 months ago (Nov. 18, 2021, 1:42 p.m.)
Deposited	3 years, 9 months ago (Nov. 18, 2021, 1:43 p.m.)
Indexed	3 weeks, 2 days ago (Aug. 7, 2025, 4:48 p.m.)
Issued	26 years, 3 months ago (May 1, 1999)
Published	26 years, 3 months ago (May 1, 1999)
Published Online	26 years, 3 months ago (May 1, 1999)
Published Print	26 years, 3 months ago (May 1, 1999)

Funders 0

None

BibTeX

@article{Brunner_1999, title={Genomic Structure and Comparative Analysis of Nine Fugu Genes: Conservation of Synteny with Human Chromosome Xp22.2–p22.1}, volume={9}, ISSN={1549-5469}, url={http://dx.doi.org/10.1101/gr.9.5.437}, DOI={10.1101/gr.9.5.437}, number={5}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Brunner, Bodo and Todt, Tilman and Lenzner, Steffen and Stout, Karen and Schulz, Ute and Ropers, Hans-Hilger and Kalscheuer, Vera M.}, year={1999}, month=may, pages={437–448} }

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