Murine segmental duplications are hot spots for chromosome and gene evolution

Genomics

Volumn 86, Issue 6, 2005, Pages 692-700

  Armengol, Lluís ^a   Marquès Bonet, Tomàs ^b   Cheung, Joseph ^c   Khaja, Razi ^c   González, Juan R ^a   Scherer, Stephen W ^c   Navarro, Arcadi ^b   Estivill, Xavier ^a  

^a Center for Genomic Regulation   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

Chromosomal evolution; Evolutionary breakpoints; Molecular evolution; Mouse genome; Rat genome; Segmental duplications; Synteny breakpoints

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; COMPARATIVE STUDY; GENE DUPLICATION; GENE REARRANGEMENT; GENETIC ANALYSIS; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; RAT; SPECIES DIFFERENTIATION; SYNTENY;

ANIMALS; CHROMOSOMES, MAMMALIAN; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE REARRANGEMENT; GENOMICS; MICE; RATS; SYNTENY;

MAMMALIA; MURINAE; RODENTIA;

EID: 28644444691     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2005.08.008     Document Type: Article

References (58)

1. J.H. Nadeau, and B.A. Taylor Lengths of chromosomal segments conserved since divergence of man and mouse Proc. Natl. Acad. Sci. U. S. A. 81 1984 814 818
2. J.H. Nadeau, and D. Sankoff The lengths of undiscovered conserved segments in comparative maps Mamm. Genome 9 1998 491 495
3. P. Pevzner, and G. Tesler Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited "RECOMB 2003," April 10-13, 2003, Max Planck Institute for Molecular Genetics and the Berlin Center for Genome-Based Bioinformatics, Berlin, Germany 2003
4. G. Bourque, P.A. Pevzner, and G. Tesler Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes Genome Res. 14 2004 507 516
5. S. Zhao, J. Shetty, L. Hou, A. Delcher, B. Zhu, and K. Osoegawa Human, mouse, and rat genome large-scale rearrangements: stability versus speciation Genome Res. 14 2004 1851 1860
6. G. Bourque, E.M. Zdobnov, P. Bork, P.A. Pevzner, and G. Tesler Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages Genome Res. 15 2005 98 110
7. W.J. Murphy, D.M. Larkin, A. Everts-van der Wind, G. Bourque, G. Tesler, and L. Auvil Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps Science 309 2005 613 617
8. P. Trinh, A. McLysaght, and D. Sankoff Genomic features in the breakpoint regions between syntenic blocks Bioinformatics 20 Suppl. 1 2004 I318 I325
9. E. Kolomietz, M.S. Meyn, A. Pandita, and J.A. Squire The role of Alu repeat clusters as mediators of recurrent chromosomal aberrations in tumors Genes Chromosomes Cancer 35 2002 97 112
10. C.J. Shaw, and J.R. Lupski Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease Hum. Mol. Genet. 1 2004 R57 R64
11. G.R. Sutherland, E. Baker, and R.I. Richards Fragile sites still breaking Trends Genet. 14 1998 501 506
12. A. Ruiz-Herrera, M. Ponsa, F. Garcia, J. Egozcue, and M. Garcia Fragile sites in human and Macaca fascicularis chromosomes are breakpoints in chromosome evolution Chromosome Res. 10 2002 33 44
13. D. Sankoff, M. Deneault, P. Turbis, and C. Allen Chromosomal distributions of breakpoints in cancer, infertility, and evolution Theor. Popul. Biol. 61 2002 497 501
14. P. Dehal, P. Predki, A.S. Olsen, A. Kobayashi, P. Folta, and S. Lucas Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution Science 293 2001 104 111
15. R. Puttagunta, L.A. Gordon, G.E. Meyer, D. Kapfhamer, J.E. Lamerdin, and P. Kantheti Comparative maps of human 19p13.3 and mouse chromosome 10 allow identification of sequences at evolutionary breakpoints Genome Res. 10 2000 1369 1380
16. M. Kost-Alimova, H. Kiss, L. Fedorova, Y. Yang, J.P. Dumanski, and G. Klein Coincidence of synteny breakpoints with malignancy-related deletions on human chromosome 3 Proc. Natl. Acad. Sci. U. S. A. 100 2003 6622 6627
17. L. Armengol, M.A. Pujana, J. Cheung, S.W. Scherer, and X. Estivill 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 2003 2201 2208
18. J.A. Bailey, R. Baertsch, W.J. Kent, D. Haussler, and E.E. Eichler Hotspots of mammalian chromosomal evolution Genome Biol. 5 2004 R23
19. P. Stankiewicz, and J.R. Lupski Molecular-evolutionary mechanisms for genomic disorders Curr. Opin. Genet. Dev. 12 2002 312 319
20. P. Stankiewicz, C.J. Shaw, J.D. Dapper, K. Wakui, L.G. Shaffer, and M. Withers Genome architecture catalyzes nonrecurrent chromosomal rearrangements Am. J. Hum. Genet. 72 2003 1101 1116
21. M. Caceres, J.M. Ranz, A. Barbadilla, M. Long, and A. Ruiz Generation of a widespread Drosophila inversion by a transposable element Science 285 1999 415 418
22. M.T. Pletcher, B.A. Roe, F. Chen, T. Do, A. Do, and E. Malaj Chromosome evolution: the junction of mammalian chromosomes in the formation of mouse chromosome 10 Genome Res. 10 2000 1463 1467
23. H. Kehrer-Sawatzki, C. Sandig, N. Chuzhanova, V. Goidts, J.M. Szamalek, and S. Tanzer Breakpoint analysis of the pericentric inversion distinguishing human chromosome 4 from the homologous chromosome in the chimpanzee (Pan troglodytes) Hum. Mutat. 25 2005 45 55
24. A. Navarro, and N.H. Barton Chromosomal speciation and molecular divergence-Accelerated evolution in rearranged chromosomes Science 300 2003 321 324
25. T. Marques-Bonet, M. Caceres, J. Bertranpetit, T.M. Preuss, J.W. Thomas, and A. Navarro Chromosomal rearrangements and the genomic distribution of gene-expression divergence in humans and chimpanzees Trends Genet. 20 2004 524 529
26. J. Zhang, X. Wang, and O. Podlaha Testing the chromosomal speciation hypothesis for humans and chimpanzees Genome Res. 14 2004 845 851
27. E.J. Vallender, N.M. Pearson, and B.T. Lahn The X chromosome: not just her brother's keeper Nat. Genet. 37 2005 343 345
28. J. Lu, W.H. Li, and C.I. Wu Comment on "Chromosomal speciation and molecular divergence-Accelerated evolution in rearranged chromosomes " Science 302 2003 988 (author reply 988)
29. X. Gu Evolution of duplicate genes versus genetic robustness against null mutations Trends Genet. 19 2003 354 356
30. Z. Gu, L.M. Steinmetz, X. Gu, C. Scharfe, R.W. Davis, and W.H. Li Role of duplicate genes in genetic robustness against null mutations Nature 421 2003 63 66
31. M.G.S. Consortium, R.H. Waterston, K. Lindblad-Toh, E. Birney, J. Rogers, and J.F. Abril Initial sequencing and comparative analysis of the mouse genome Nature 420 2002 520 562
32. R.G.S. Consortium, R.A. Gibbs, G.M. Weinstock, M.L. Metzker, D.M. Muzny, and E.J. Sodergren Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428 2004 493 521
33. S. Ohno Ancient linkage groups and frozen accidents Nature 244 1973 259 262
34. P. Pevzner, and G. Tesler Genome rearrangements in mammalian evolution: lessons from human and mouse genomes Genome Res. 13 2003 37 45
35. J. Cheung, M.D. Wilson, J. Zhang, R. Khaja, J.R. MacDonald, and H.H. Heng Recent segmental and gene duplications in the mouse genome Genome Biol. 4 2003 R47
36. E. Tuzun, J.A. Bailey, and E.E. Eichler Recent segmental duplications in the working draft assembly of the brown Norway rat Genome Res. 14 2004 493 506
37. E.E. Eichler Masquerading repeats: paralogous pitfalls of the human genome Genome Res. 8 1998 758 762
38. J. Cheung, X. Estivill, R. Khaja, J.R. MacDonald, K. Lau, and L.C. Tsui Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence Genome Biol. 4 2003 R25
39. X. She, Z. Jiang, R.A. Clark, G. Liu, Z. Cheng, and E. Tuzun Shotgun sequence assembly and recent segmental duplications within the human genome Nature 431 2004 927 930
40. J.A. Bailey, A.M. Yavor, H.F. Massa, B.J. Trask, and E.E. Eichler Segmental duplications: organization and impact within the current human genome project assembly Genome Res. 11 2001 1005 1017
41. F.C. Chen, and W.H. Li Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees Am. J. Hum. Genet. 68 2001 444 456
42. J. Castresana Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content Nucleic Acids Res. 30 2002 1751 1756
43. M. Lynch, and J.S. Conery The evolutionary fate and consequences of duplicate genes Science 290 2000 1151 1155
44. V.E. Prince, and F.B. Pickett Splitting pairs: the diverging fates of duplicated genes Nat. Rev. Genet. 3 2002 827 837
45. W.J. Murphy, R. Stanyon, and S.J. O'Brien Evolution of mammalian genome organization inferred from comparative gene mapping Genome Biol. 2 2001 (REVIEWS0005)
46. S.J. O'Brien, M. Menotti-Raymond, W.J. Murphy, W.G. Nash, J. Wienberg, R. Stanyon, The promise of comparative genomics in mammals. Science 286 (1999) 458-462, 479-481.
47. J.M. Carlton, S.V. Angiuoli, B.B. Suh, T.W. Kooij, M. Pertea, and J.C. Silva Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii Nature 419 2002 512 519
48. A. Coghlan, and K.H. Wolfe Fourfold faster rate of genome rearrangement in nematodes than in Drosophila Genome Res. 12 2002 857 867
49. M. Kellis, N. Patterson, M. Endrizzi, B. Birren, and E.S. Lander Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 423 2003 241 254
50. E. Nickerson, and D.L. Nelson Molecular definition of pericentric inversion breakpoints occurring during the evolution of humans and chimpanzees Genomics 50 1998 368 372
51. R.V. Samonte, and E.E. Eichler Segmental duplications and the evolution of the primate genome Nat. Rev. Genet 3 2002 65 72
52. D.P. Locke, N. Archidiacono, D. Misceo, M.F. Cardone, S. Deschamps, and B. Roe Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster Genome Biol. 4 2003 R50
53. V. Goidts, J.M. Szamalek, H. Hameister, and H. Kehrer-Sawatzki Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates Hum. Genet. 115 2004 116 122
54. W.J. Murphy, R. Agarwala, A.A. Schaffer, R. Stephens, C. Smith, and N.J. Crumpler Jr. A rhesus macaque radiation hybrid map and comparative analysis with the human genome Genomics 2005
55. Y. Zhou, and B. Mishra Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling Proc. Natl. Acad. Sci. U. S. A. 102 2005 4051 4056
56. S. Schwartz, W.J. Kent, A. Smit, Z. Zhang, R. Baertsch, and R.C. Hardison Human-mouse alignments with BLASTZ Genome Res. 13 2003 103 107
57. P. Pevzner, and G. Tesler Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution Proc. Natl. Acad. Sci. U. S. A. 100 2003 7672 7677
58. P. Good Permutation Tests 2000 Springer-Verlag New York