Recent segmental duplications in the working draft assembly of the brown Norway rat

Genome Research

Volumn 14, Issue 4, 2004, Pages 493-506

  Tuzun, Eray ^a   Bailey, Jeffrey A ^a   Eichler, Evan E ^a  

^a UNIVERSITY HOSPITALS OF CLEVELAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; CHROMOSOME DUPLICATION; CHROMOSOME STRUCTURE; CONTROLLED STUDY; DNA FLANKING REGION; EXON; GENE CLUSTER; GENE IDENTIFICATION; GENE SEQUENCE; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ANIMALS; BASE COMPOSITION; CHROMOSOMES; COMPUTATIONAL BIOLOGY; CONTIG MAPPING; GENE CONVERSION; GENE DUPLICATION; GENES; GENOME; RATS; RATS, INBRED BN;

RATTUS; RATTUS NORVEGICUS;

EID: 1842717953     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1907504     Document Type: Article

References (36)

1. Atchison, M. and Adesnik, M. 1986. Gene conversion in a cytochrome P-450 gene family. Proc. Natl. Acad. Sci. 83: 2300-2304.
2. Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J., and Eichler, E.E. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11: 1005-1017.
3. Bailey, J.A., Gu, Z., Clark, R.A., Reinert, K., Samonte, R.V., Schwartz, S., Adams, M.D., Myers, E.W., Li, P.W., and Eichler, E.E. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007.
4. Bailey, J.A., Giu, L., and Eichler, E.E. 2003. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73: 823-834.
5. Cheung, J., Estivill, X., Khaja, R., MacDonald, J.R., Lau, K., Tsui, L.C., and Scherer, S.W. 2003a. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4: R25.
6. Cheung, J., Wilson, M.D., Zhang, J., Khaja, R., MacDonald, J.R., Heng, H.H., Koop, B.F., and Scherer, S.W. 2003b. Recent segmental and gene duplications in the mouse genome. Genome Biol. 4: R47.
7. Cheung, V.G., Nowak, N., Jang, W., Kirsch, I.R., Zhao, S., Chen, X.N., Furey, T.S., Kim, U.J., Kuo, W.L., Olivier, M., et al. 2001. Integration of cytogenetic landmarks into the draft sequence of the human genome. The BAC Resource Consortium. Nature 409: 953-958.
8. Dehal, P., Predki, P., Olsen, A.S., Kobayashi, A., Folta, P., Lucas, S., Land, M., Terry, A., Zhou, C.L.E., Rash, S., et al. 2001. Human chromosome 19 and related regions in mouse: Conservative and lineage specific evolution. Science 293: 104-111.
9. Dubois, J.Y., Jekel, P.A., Mulder, P.P., Bussink, A.P., Catzeflis, F.M., Carsana, A., and Beintema, J.J. 2002. Pancreatic-type ribonuclease 1 gene duplications in rat species. J. Mol. Evol. 55: 522-533.
10. Duda, T.F. and Palumbi, S.R. 1999. Molecular genetics of ecological diversification: Duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc. Natl. Acad. Sci. 96: 6820-6823.
11. Eichler, E.E. 1998. Masquerading repeats: Paralogous pitfalls of the human genome. Genome Res. 8: 758-762.
12. Eichler, E.E. 2001. Segmental duplications: What's missing, misassigned, and misassembled - And should we care? Genome Res. 11: 653-656.
13. Eichler, E.E. and Sankoff, D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301: 793-797.
14. Eichler, E.E., Lu, F., Shen, Y., Antonacci, R., Jurecic, V., Doggett, N.A., Moyzis, R.K., Baldini, A., Gibbs, R.A., and Nelson, D.L. 1996. Duplication of a gene-rich cluster between 16p11.1 and Xq28: A novel pericentromeric-directed mechanism for paralogous genome evolution. Hum. Mol. Genet. 5: 899-912.
15. Estivill, X., Cheung, J., Pujana, M.A., Nakabayashi, K., Scherer, S.W., and Tsui, L.C. 2002. Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum. Mol. Genet. 11: 1987-1995.
16. Goodier, J.L., Ostertag, E.M., and Kazazian Jr., H.H. 2000. Transduction of 3′-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9: 653-657.
17. Horvath, J., Schwartz, S., and Eichler, E. 2000. The mosaic structure of a 2p11 pericentromeric segment: A strategy for characterizing complex regions of the human genome. Genome Res. 10: 839-852.
18. International Human Genome Sequencing Consortium (IHGSC). 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-920.
19. Ioannidu, S., Walter, L., Dressel, R., and Gunther, E. 2001. Physical map and expression profile of genes of the telomeric class I gene region of the rat MHC. J. Immunol. 166: 3957-3965.
20. Jackson, M.S., Rocchi, M., Thompson, G., Hearn, T., Crosier, M., Guy, J., Kirk, D., Mulligan, L., Ricco, A., Piccininni, S., et al. 1999. Sequences flanking the centromere of human chromosome 10 are a complex patchwork of arm-specific sequences, stable duplications, and unstable sequences with homologies to telomeric and other centromeric locations. Hum. Mol. Genet. 8: 205-215.
21. Jacob, H.J. and Kwitek, A.E. 2002. Rat genetics: Attaching physiology and pharmacology to the genome. Nat. Rev. Genet. 3: 33-42.
22. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
23. Kent, WJ., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res. 12: 996-1006.
24. McFadyen, D.A. and Locke, J. 2000. High-resolution FISH mapping of the rat α2u-globulin multigene family. Mamm. Genome 11: 292-299.
25. McFadyen, D.A., Addison, W., and Locke, J. 1999. Genomic organization of the rat α2u-globulin gene cluster. Mamm. Genome 10: 463-470.
26. Muller, H.J. 1936. Bar duplication. Science 83: 528-530.
27. Ohno, S. 1970. Evolution by gene duplication. Springer Verlag, Berlin.
28. Oldfield, S., Grubb, B.D., and Donaldson, L.F. 2001. Identification of a prostaglandin E2 receptor splice variant and its expression in rat tissues. Prostaglandins 63: 165-173.
29. Pages, G., Rouayrenc, J.F., Rossi, V., Le Cam, G., Mariller, M., Szpirer, J., Szpirer, C., Levan, G., and Le Cam, A. 1990. Primary structure and assignment to chromosome 6 of three related rat genes encoding liver serine protease inhibitors. Gene 94: 273-282.
30. Pickeral, O.K., Makalowski, W., Boguski, M.S., and Boeke, J.D. 2000. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 10: 411-415.
31. Rat Genome Sequencing Project Consortium (RGSPC). 2004. Genome sequence of the Brown Norway Rat yields insights into mammalian evolution. Nature (in press).
32. Rolstad, B., Naper, C., Lovik, G., Vaage, J.T., Ryan, J.C., Backman-Petersson, E., Kirsch, R.D., and Butcher, G.W. 2001. Rat natural killer cell receptor systems and recognition of MHC class I molecules. Immunol. Rev. 181: 149-157.
33. Springer, M.S., Murphy, W.J., Eizirik, E., and O'Brien, S.J. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. 100: 1056-1061.
34. Thomas, J.W., Schueler, M.G., Summers, T.J., Blakesley, R.W., McDowell, J.C., Thomas, P.J., Idol, J.R., Maduro, V.V., Lee-Lin, S.Q., Touchman, J.W., et al. 2003. Pericentromeric duplications in the laboratory mouse. Genome Res. 13: 55-63.
35. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
36. Yan, B., Yang, D., and Parkinson, A. 1995. Cloning and expression of hydrolase C, a member of the rat carboxylesterase family. Arch. Biochem. Biophys. 317: 222-234.