Analysis of segmental duplications and genome assembly in the mouse

Genome Research

Volumn 14, Issue 5, 2004, Pages 789-801

  Bailey, Jeffrey A ^a   Church, Deanna M ^b   Ventura, Mario ^c   Rocchi, Mariano ^c   Eichler, Evan E ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c UNIVERSITY OF BARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; COMPARATIVE STUDY; GENE ASSIGNMENT; GENE DUPLICATION; GENE INSERTION; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; MAMMAL; MOUSE; MOUSE STRAIN; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; UNINDEXED SEQUENCE;

ANIMALS; BASE COMPOSITION; BONE MARROW CELLS; CELL NUCLEUS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENE DUPLICATION; GENES; GENOME; GENOME, HUMAN; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICE; MICE, INBRED C57BL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

MAMMALIA;

EID: 2442680252     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2238404     Document Type: Article

References (51)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol, Biol. 215: 403-410.
2. Armengol, L., Pujana, M.A., Cheung, J., Scherer, S.W., and Estivill, X. 2003. Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum. Mol. Genet. 12: 2201-2208.
3. 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.
4. 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. 2002a. Recent segmental duplications in the human genome. Science 297: 1003-1007.
5. Bailey, J.A., Yavor, A.M., Viggiano, L., Misceo, D., Horvath, J.E., Archidiacono, N., Schwartz, S., Rocchi, M., and Eichler, E.E. 2002b. Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70: 83-100.
6. Bailey, J.A., Liu, G., 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.
7. Batzoglou, S., Jaffe, D.B., Stanley, K., Butler, J., Gnerre, S., Mauceli, E., Berger, B., Mesirov, J.P., and Lander, E.S. 2002. ARACHNE: A whole-genome shotgun assembler. Genome Res. 12: 177-189.
8. Cheung, V.E., 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. Nature 409: 953-958.
9. 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.
10. Cheung, J., Wilson, M.D., Zhang, J., Khaia, 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.
11. Collins, F.S., Green, E.D., Guttmacher, A.E., and Guyer, M.S. 2003. A vision for the future of genomics research. Nature 422: 835-847.
12. Copley, R.R., Goodstadt, L., and Pouting, C. 2003. Eukaryotic domain evolution inferred from genome comparisons. Curr. Opin. Genet. Dev. 13: 623-628.
13. DeBerardinis, R.J., Goodier, J.L., Ostertag, E.M., and Kazazian Jr., H.H. 1998. Rapid amplification of a retrotransposon subfamily is evolving the mouse genome. Nat.,Genet. 20: 288-290.
14. 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.
15. DiDonato, C.J., Chen, X.N., Noya, D., Korenberg, J.R., Nadeau, J.H., and Simard, L.R. 1997. Cloning, characterization, and copy number of the murine survival motor neuron gene: Homolog of the spinal muscular atrophy-determining gene. Genome Res. 7: 339-352.
16. Eichler, E.E. 1998. Masquerading repeats: Paralogous pitfalls of the Human Genome. Genome Res. 8: 758-762.
17. Eichler, E.E. 1999. Repetitive conundrums of centromere structure and function. Hum. Mol. Genet. 8: 151-155.
18. Eichler, E.E. 2001. Segmental duplications: What's missing, misassigned, and misassembled - And should we care? Genome Res. 11: 653-656.
19. Eichler, E.E. and Sankoff, D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301: 793-797.
20. 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 nucleoticle polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum. Mol. Genet. 11: 1987-1995.
21. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
22. Giglio, S., Calvari, V., Gregato, G., Gimelli, G., Camanini, S., Giorda, R., Ragusa, A., Guerneri, S., Selicorni, A., Stumm, M., et al. 2002. Heterozygous submicroscopic inversions involving olfactory receptor-gene clusters mediate the recurrent t(4;8)(p16;p23) translocation. Am. J. Hum. Genet. 71: 276-285.
23. Gimelli, G., Pujana, M.A., Patricelli, M.G., Russo, S., Giardino, D., Larizza, L., Cheung, J., Armengol, L., Schinzel, A., Estivill, X., et al. 2003. Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum. Mol. Genet. 12: 849-858.
24. Green, P. 1997. Against a whole-genome shotgun. Genome Res. 7: 410-417.
25. International Human Genome Sequencing Consortium (IHGSC). 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
26. Ji, Y., Walkowicz, M.J., Buiting, K., Johnson, D.K., Tarvin, R.E., Rinchik, E.M., Horsthernke, B., Stubbs, L., and Nicholls, R.D. 1999. The ancestral gene for transcribed, low-copy repeats in the Prader-Willi/Angelman region encodes a large protein implicated in protein trafficking, which is deficient in mice with neuromuscular and spermiogenic abnormalities. Hum. Mol. Genet. 8: 533-542.
27. Ji, Y., Eichler, E.E., Schwartz, S., and Nicholls, R.D. 2000. Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10: 597-610.
28. Johnson, M.E., Viggiano, L., Bailey, J.A., Abdul-Rauf, M., Goodwin, G., Rocchi, M., and Eichler, E.E. 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature 413: 514-519.
29. Kazazian Jr., H.H. 2000. Genetics. L1 retrotransposons shape the mammalian genome. Science 289: 1152-1153.
30. Lichter, P., Tang, C.J., Call, K., Hermanson, G., Evans, G.A., Housman, D., and Ward, D.C. 1990. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64-69.
31. Locke, D.P., Archidiacono, N., Misceo, D., Cardone, M.F., Dechamps, S., Roe, B.A., Rocchi, M., and Eichler, E.E. 2003. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol. 4: R50.
32. Lupski, J.R. 1998. Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14: 417-422.
33. Mears, M.L. and Hutchison III, C.A. 2001. The evolution of modern lineages of mouse L1 elements. J. Mol. Evol. 52: 51-62.
34. Mouse Genome Sequencing Consortium (MGSC). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
35. Muller, H.J. 1936. Bar duplication. Science 83: 528-530.
36. Mural, R.J., Adams, M.D., Myers, E.W., Smith, H.O., Miklos, G.L., Wides, R., Halpern, A., Li, P.W., Sutton, G.G., Nadeau, J., et al. 2002. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661-1671.
37. Ohno, S., Wolf, U., and Atkin, N. 1968. Evolution from fish to mammals by gene duplication. Hereditas 59: 169-187.
38. Osborne, L.R., Li, M., Pober, B., Chitayat, D., Bodurtha, J., Mandel, A., Costa, T., Grebe, T., Cox, S., Tsui, L.C., et al. 2001. A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nat. Genet. 29: 321-325.
39. Paulding, C.A., Ruvolo, M., and Haber, D.A. 2003. The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc. Natl. Acad. Sci. 100: 2507-2511.
40. Pentao, L., Wise, C., Chinault, A., Patel, P., and Lupski, J. 1992. Charcot-Marie-Tooth type 1A duplication appears to arise from recombination at repeat sequences flanking the 1.5 Mb monomer unit. Nat. Genet. 2: 292-300.
41. Probst, F.J., Chen, K.S., Zhao, Q., Wang, A., Friedman, T.B., Lupski, J.R., and Camper, S.A. 1999. A physical map of the mouse shaker-2 region contains many of the genes commonly deleted in Smith-Magenis syndrome (del17p11.2p11.2). Genomics 55: 348-352.
42. Samonte, R., Conte, R., Ramesh, K., and Verma, R. 1996. Molecular cytogenetic characterization of breakpoints involving pericentric inversions of human chromosome 9. Hum. Genet. 98: 576-580.
43. Samonte, R.V. and Eichler, E.E. 2002. Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3: 65-72.
44. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
45. Sprenger, R., Schlagenhaufer, R., Kerb, R., Bruhn, C., Brockmoller, J., Roots, I., and Brinkman, U. 2000. Characterization of the glutathione S-transferase GSTT1 deletion: Discrimination of all genotypes by polymerase chain reaction indicates a trimodular genotype-phenotype correlation. Pharmacogenetics 10: 557-565.
46. Stankiewicz, P., Park, S.S., Inoue, K., and Lupski, J.R. 2001. The evolutionary chromosome translocation 4;19 in Gorilla gorilla is associated with microduplication of the chromosome fragment syntenic to sequences surrounding thr human proximal CMT1A-REP. Genome Res. 11: 1205-1210.
47. Thomas, J.W., Schueler, M.G., Summers, T.J., Blakesly, 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.
48. Tusun E., Bailey, J., and Eichler, E.E. 2004. Recent segmental duplication in the working draft assembly of the brown Norway rat. Genome Res. 14: 493-506.
49. van der Weyden, L., Adams, D.J., and Bradley, A. 2002. Tools for targeted manipulation of the mouse genome. Physiol. Genomics 11: 133-164.
50. Venter, J.C., Adams, M.D., Myers, E.W., Li, R.J., Mural, P.W., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A. et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
51. Weber, J.L. and Myers, E.W. 1997. Human whole-genome shotgun sequencing. Genome Res. 7: 401-409.