Analysis of recent segmental duplications in the bovine genome

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Liu, George E ^a   Ventura, Mario ^b   Cellamare, Angelo ^b   Chen, Lin ^c   Cheng, Ze ^c   Zhu, Bin ^d   Li, Congjun ^a   Song, Jiuzhou ^d   Eichler, Evan E ^c,e  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF BARI   (Italy)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF MARYLAND   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BOS TAURUS; CATTLE; CHROMOSOME DUPLICATION; CONTROLLED STUDY; DNA FLANKING REGION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CONVERSION; GENETIC ASSOCIATION; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENTIATION; ANIMAL; CELL LINE; DOG; GENETICS; GENOME; GENOMICS; HUMAN; MALE; MOUSE; NUCLEOTIDE REPEAT; RAT;

BOS; BOS TAURUS; BOVINAE; HOMINIDAE; MAMMALIA; PRIMATES; RODENTIA;

ANIMALS; CATTLE; CELL LINE; DOGS; GENOME; GENOMICS; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; MICE; RATS; SEGMENTAL DUPLICATIONS, GENOMIC;

EID: 73149108420     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-571     Document Type: Article

References (62)

1. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S. Recent segmental duplications in the human genome. Science 2002, 297:1003-7. 10.1126/science.1072047, 12169732.
2. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 2005, 437:88-93. 10.1038/nature04000, 16136132.
3. Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE. Analysis of segmental duplications and genome assembly in the mouse. Genome Res 2004, 14:789-801. 10.1101/gr.2238404, 479105, 15123579.
4. Tuzun E, Bailey JA, Eichler EE. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res 2004, 14:493-506. 10.1101/gr.1907504, 383293, 15059990.
5. Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, Heng HH. Recent segmental and gene duplications in the mouse genome. Genome Biol 2003, 4:R47. 10.1186/gb-2003-4-8-r47, 193640, 12914656.
6. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol 2003, 4:R25. 10.1186/gb-2003-4-4-r25, 154576, 12702206.
7. She X, Cheng Z, Zollner S, Church DM, Eichler EE. Mouse segmental duplication and copy number variation. Nat Genet 2008, 40:909-914. 10.1038/ng.172, 2574762, 18500340.
8. Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM. The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res 2009, 19:491-499. 10.1101/gr.084715.108, 2661811, 19129542.
9. Ohno S. Evolution by Gene Duplication 1970, Berlin/Heidelberg/New York: Springer Verlag.
10. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005, 77:78-88. 10.1086/431652, 1226196, 15918152.
11. Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 2007, 3:e3. 10.1371/journal.pgen.0030003, 1761046,1761046, 17206864.
12. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD. Global variation in copy number in the human genome. Nature 2006, 444:444-454. 10.1038/nature05329, 2669898, 17122850.
13. Duda TF, Palumbi SR. Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc Natl Acad Sci USA 1999, 96:6820-3. 10.1073/pnas.96.12.6820, 21999, 10359796.
14. Eichler EE, Sankoff D. Structural dynamics of eukaryotic chromosome evolution. Science 2003, 301:793-797. 10.1126/science.1086132, 12907789.
15. Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S. Human chromosome 19 and related regions in mouse: conservative and lineage specific evolution. Science 2001, 293:104-111. 10.1126/science.1060310, 11441184.
16. Murphy WJ, Larkin DM, Wind A, Bourque G, Tesler G, Auvil L. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 2005, 309:613-617. 10.1126/science.1111387, 16040707.
17. Armengol L, Pujana MA, Cheung J, Scherer SW, Estivill X. 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 2003, 12:2201-2208. 10.1093/hmg/ddg223, 12915466.
18. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biol 2004, 5:R23. 10.1186/gb-2004-5-4-r23, 395782, 15059256.
19. Emanuel BS, Shaikh TH. Segmental duplications: an 'expanding' role in genomic instability and disease. Nat Rev Genet 2001, 2:791-800. 10.1038/35093500, 11584295.
20. Bailey JA, Eichler EE. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet 2006, 7:552-564. 10.1038/nrg1895, 16770338.
21. Eichler EE. Widening the spectrum of human genetic variation. Nat Genet 2006, 38:9-11. 10.1038/ng0106-9, 16380720.
22. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006, 7:85-97. 10.1038/nrg1767, 16418744.
23. Beckmann JS, Estivill X, Antonarakis SE. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 2007, 8:639-646. 10.1038/nrg2149, 17637735.
24. Conrad B, Antonarakis SE. Gene duplication: a drive for phenotypic diversity and cause of human disease. Annu Rev Genomics Hum Genet 2007, 8:17-35. 10.1146/annurev.genom.8.021307.110233, 17386002.
25. Sebat J. Major changes in our DNA lead to major changes in our thinking. Nat Genet 2007, 39:S3-S5. 10.1038/ng2095, 17597778.
26. Eichler EE. Segmental duplications: what's missing, misassigned, and misassembled- and should we care?. Genome Res 2001, 11:653-6. 10.1101/gr.188901, 11337463.
27. Estivill X, Cheung J, Pujana MA, Nakabayashi K, Scherer SW, Tsui LC. Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum Mol Genet 2002, 11:1987-1995. 10.1093/hmg/11.17.1987, 12165560.
28. She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun E. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 2004, 431:927-930. 10.1038/nature03062, 15496912.
29. The Bovine Genome Sequencing and Analysis Consortium The Genome Sequence of Taurine Cattle: a window to ruminant biology and evolution. Science 2009, 324:522-528. 10.1126/science.1169588, 19390049.
30. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 2009, 10:R42. 10.1186/gb-2009-10-4-r42, 2688933, 19393038.
31. Eichler EE. Repetitive conundrums of centromere structure and function. Hum Mol Genet 1999, 8:151-155. 10.1093/hmg/8.2.151, 9931322.
32. Collins FS, Green ED, Guttmacher AE, Guyer MS. A vision for the future of genomics research. Nature 2003, 422:835-847. 10.1038/nature01626, 12695777.
33. Eck S, Benet-Pages A, Flisikowski K, Meitinger T, Fries R, Strom TM. Whole genome sequencing of a single Bos taurus animal for SNP discovery. Genome Biol 2009, 10:R82. 10.1186/gb-2009-10-8-r82, 2745763, 19660108.
34. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 2001, 11:1005-17. 10.1101/gr.GR-1871R, 311093, 11381028.
35. Bailey JA, Liu G, Eichler EE. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 2003, 73:823-834. 10.1086/378594, 1180605, 14505274.
36. Stankiewicz P, Park SS, Inoue K, Lupski JR. The evolutionary chromosome translocation 4;19 in Gorilla gorilla is associated with microduplication of the chromosome fragment syntenic to sequences surrounding the human proximal CMT1A-REP. Genome Res 2001, 11:1205-10. 10.1101/gr.181101, 311135, 11435402.
37. Locke DP, Archidiacono N, Misceo D, Cardone MF, Deschamps S, Roe B. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol 2003, 4:R50. 10.1186/gb-2003-4-8-r50, 193642, 12914658.
38. Nei M, Rooney AP. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 2005, 39:121-152. 10.1146/annurev.genet.39.073003.112240, 1464479, 16285855.
39. Cho S, Zhang J. Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals. Gene 2006, 373:116-125. 10.1016/j.gene.2006.01.018, 16530354.
40. Nei M, Niimura Y, Nozawa M. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 2008, 9:951-963. 10.1038/nrg2480, 19002141.
41. Patil AA, Cai Y, Sang Y, Blecha F, Zhang G. Cross-species analysis of the mammalian beta-defensin gene family: presence of syntenic gene clusters and preferential expression in the male reproductive tract. Physiol Genomics 2005, 23:5-17. 10.1152/physiolgenomics.00104.2005, 16033865.
42. Radhakrishnan Y, Fares MA, French FS, Hall SH. Comparative genomic analysis of a mammalian beta-defensin gene cluster. Physiol Genomics 2007, 30:213-222. 10.1152/physiolgenomics.00263.2006, 17456736.
43. Thomas JH. Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PLoS Genet 2007, 3:e67. 10.1371/journal.pgen.0030067, 1866355,1866355, 17500592.
44. Woelk CH, Frost SD, Richman DD, Higley PE, Kosakovsky Pond SL. Evolution of the interferon alpha gene family in eutherian mammals. Gene 2007, 397:38-50. 10.1016/j.gene.2007.03.018, 2174272, 17512142.
45. Walker AM, Roberts RM. Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies. BMC Genomics 2009, 10:187. 10.1186/1471-2164-10-187, 2680415, 19393062.
46. Connelley T, Aerts J, Law A, Morrison WI. Genomic analysis reveals extensive gene duplication within the bovine TRB locus. BMC Genomics 2009, 10:192. 10.1186/1471-2164-10-192, 2685407, 19393068.
47. Wheeler TT, Hood KA, Maqbool NJ, McEwan JC, Bingle CD, Zhao S. Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle. BMC Genomics 2007, 8:75. 10.1186/1471-2164-8-75, 1839098, 17362520.
48. Telugu BP, Walker AM, Green JA. Characterization of the bovine pregnancy-associated glycoprotein gene family--analysis of gene sequences, regulatory regions within the promoter and expression of selected genes. BMC Genomics 2009, 10:185. 10.1186/1471-2164-10-185, 2682831, 19393060.
49. Larson JH, Marron BM, Beever JE, Roe BA, Lewin HA. Genomic organization and evolution of the ULBP genes in cattle. BMC Genomics 2006, 7:227. 10.1186/1471-2164-7-227, 1574312, 16953885.
50. Herzig CT, Baldwin CL. Genomic organization and classification of the bovine WC1 genes and expression by peripheral blood gamma delta T cells. BMC Genomics 2009, 10:191. 10.1186/1471-2164-10-191, 2681482, 19393067.
51. Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN. Integration of cytogenetic landmarks into the draft sequence of the human genome. The BAC Resource Consortium. Nature 2001, 409:953-8. 10.1038/35057192, 11237021.
52. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004, 428:493-521. 10.1038/nature02426, 15057822.
53. Liu G, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP. Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. BMC Genomics 2006, 7:140. 10.1186/1471-2164-7-140, 1525190, 16759380.
54. Kijas JW, Menzies M, Ingham A. Sequence diversity and rates of molecular evolution between sheep and cattle genes. Anim Genet 2006, 37:171-174. 10.1111/j.1365-2052.2005.01399.x, 16573533.
55. Stewart CB, Schilling JW, Wilson AC. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 1987, 330:401-404. 10.1038/330401a0, 3120013.
56. Irwin DM. Molecular evolution of ruminant lysozymes. EXS 1996, 75:347-361.
57. Irwin DM. Evolution of the bovine lysozyme gene family: changes in gene expression and reversion of function. J Mol Evol 1995, 41:299-312. 10.1007/BF01215177, 7563116.
58. Rocchi M, Archidiacono N, Stanyon R. Ancestral genomes reconstruction: an integrated, multi-disciplinary approach is needed. Genome Res 2006, 16:1441-1444. 10.1101/gr.5687906, 17053088.
59. Roberto R, Misceo D, D'Addabbo P, Archidiacono N, Rocchi M. Refinement of macaque synteny arrangement with respect to the official rheMac2 macaque sequence assembly. Chromosome Res 2008, 16:977-985. 10.1007/s10577-008-1255-1, 18841486.
60. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM. Fine-scale structural variation of the human genome. Nat Genet 2005, 37:727-732. 10.1038/ng1562, 15895083.
61. Sonstegard TS, Lopez-Corrales NL, Kappes SM, Stone RT, Ambady S, Ponce de Leon FA. An integrated genetic and physical map of the bovine X chromosome. Mamm Genome 1997, 8:16-20. 10.1007/s003359900339, 9021142.
62. Ventura M, Mudge JM, Palumbo V, Burn S, Blennow E, Pierluigi M. Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res 2003, 13:2059-2068. 10.1101/gr.1155103, 403685, 12915487.