Molecular trajectories leading to the alternative fates of duplicate genes

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Marotta, Michael ^a   Piontkivska, Helen ^b   Tanaka, Hisashi ^a  

^a LERNER RESEARCH INSTITUTE   (United States)

^b KENT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA FOOTPRINTING; DNA SEQUENCE; EVOLUTION; GENE CONVERSION; GENE DUPLICATION; GENE EXPRESSION; GENE MUTATION; GENETIC POLYMORPHISM; GENOME; GLUTATHIONE S TRANSFERASE THETA 2 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; PROMOTER REGION; SPECIES DIVERSITY;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; GENE DUPLICATION; GENE EXPRESSION; GENE SILENCING; GLUTATHIONE TRANSFERASE; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION; PAN TROGLODYTES; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84862250039     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038958     Document Type: Article

References (72)

1. Ohno S, (1970) Evolution by gene duplication. Berlin, New York,: Springer-Verlag. xv, 160 p.
2. Force A, Lynch M, Pickett FB, Amores A, Yan YL, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
3. Prince VE, Pickett FB, (2002) Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 3: 827-837.
4. Hurles M, (2004) Gene duplication: the genomic trade in spare parts. PLoS Biol 2: E206.
5. Lynch M, (2007) The origins of genome architecture. Sunderland, Mass.: Sinauer Associates. xvi, 494 p.
6. Conant GC, Wolfe KH, (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9: 938-950.
7. Taylor JS, Raes J, (2004) Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38: 615-643.
8. Kaessmann H, (2010) Origins, evolution, and phenotypic impact of new genes. Genome Res 20: 1313-1326.
9. Innan H, Kondrashov F, (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11: 97-108.
10. Wolfe KH, Shields DC, (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
11. Vision TJ, Brown DG, Tanksley SD, (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
12. Meyer A, Van de Peer Y, (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays 27: 937-945.
13. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. (2002) Recent segmental duplications in the human genome. Science 297: 1003-1007.
14. Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, et al. (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877-881.
15. Marques-Bonet T, Girirajan S, Eichler EE, (2009) The origins and impact of primate segmental duplications. Trends Genet 25: 443-454.
16. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, et al. (2005) Fine-scale structural variation of the human genome. Nat Genet 37: 727-732.
17. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
18. Bailey JA, Eichler EE, (2006) Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet 7: 552-564.
19. Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, et al. (2004) Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2: E207.
20. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, et al. (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437: 88-93.
21. Nozawa M, Kawahara Y, Nei M, (2007) Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci U S A 104: 20421-20426.
22. Kimura M, Ota T, (1974) On some principles governing molecular evolution. Proc Natl Acad Sci U S A 71: 2848-2852.
23. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV, (2002) Selection in the evolution of gene duplications. Genome Biol 3: RESEARCH0008.
24. Shiu SH, Byrnes JK, Pan R, Zhang P, Li WH, (2006) Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci U S A 103: 2232-2236.
25. Bergthorsson U, Andersson DI, Roth JR, (2007) Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A 104: 17004-17009.
26. Lynch M, Conery JS, (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
27. Walsh JB, (1995) How often do duplicated genes evolve new functions? Genetics 139: 421-428.
28. McClintock JM, Kheirbek MA, Prince VE, (2002) Knockdown of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention. Development 129: 2339-2354.
29. Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, et al. (2005) Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 37: 630-635.
30. Zhang J, Zhang YP, Rosenberg HF, (2002) Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet 30: 411-415.
31. Piatigorsky J, O'Brien WE, Norman BL, Kalumuck K, Wistow GJ, et al. (1988) Gene sharing by delta-crystallin and argininosuccinate lyase. Proc Natl Acad Sci U S A 85: 3479-3483.
32. Kleinjan DA, Bancewicz RM, Gautier P, Dahm R, Schonthaler HB, et al. (2008) Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. PLoS Genet 4: e29.
33. Nei M, Rooney AP, (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39: 121-152.
34. Gazave E, Darre F, Morcillo-Suarez C, Petit-Marty N, Carreno A, et al. (2011) Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res 21: 1626-1639.
35. Goidts V, Armengol L, Schempp W, Conroy J, Nowak N, et al. (2006) Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum Genet 119: 185-198.
36. Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, et al. (2003) Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res 13: 347-357.
37. Wilson GM, Flibotte S, Missirlis PI, Marra MA, Jones S, et al. (2006) Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res 16: 173-181.
38. Newman TL, Tuzun E, Morrison VA, Hayden KE, Ventura M, et al. (2005) A genome-wide survey of structural variation between human and chimpanzee. Genome Res 15: 1344-1356.
39. Gokcumen O, Lee C, (2009) Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization. Methods 49: 18-25.
40. Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, et al. (2008) Copy number variation and evolution in humans and chimpanzees. Genome Res 18: 1698-1710.
41. Sikela JM, (2006) The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain. PLoS Genet 2: e80.
42. Landi S, (2000) Mammalian class theta GST and differential susceptibility to carcinogens: a review. Mutat Res 463: 247-283.
43. Frova C, (2006) Glutathione transferases in the genomics era: new insights and perspectives. Biomol Eng 23: 149-169.
44. Parl FF, (2005) Glutathione S-transferase genotypes and cancer risk. Cancer Lett 221: 123-129.
45. Matejcic M, Li D, Prescott NJ, Lewis CM, Mathew CG, et al. (2011) Association of a deletion of GSTT2B with an altered risk of oesophageal squamous cell carcinoma in a South African population: a case-control study. PLoS One 6: e29366.
46. Zhao Y, Marotta M, Eichler EE, Eng C, Tanaka H, (2009) Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes. PLoS Genet 5: e1000472.
47. Tanaka H, Bergstrom DA, Yao MC, Tapscott SJ, (2005) Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification. Nat Genet 37: 320-327.
48. Gilad Y, Oshlack A, Rifkin SA, (2006) Natural selection on gene expression. Trends Genet 22: 456-461.
49. Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y, (2008) Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet 4: e1000271.
50. Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, et al. (2003) Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A 100: 13030-13035.
51. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, et al. (2003) Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423: 873-876.
52. Consortium CsaA, (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
53. Pemble SE, Taylor JB, (1992) An evolutionary perspective on glutathione transferases inferred from class-theta glutathione transferase cDNA sequences. Biochem J 287 (Pt 3): 957-963.
54. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
55. Rossjohn J, McKinstry WJ, Oakley AJ, Verger D, Flanagan J, et al. (1998) Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site. Structure 6: 309-322.
56. Tan KL, Board PG, (1996) Purification and characterization of a recombinant human Theta-class glutathione transferase (GSTT2-2). Biochem J 315 (Pt 3): 727-732.
57. Isken O, Maquat LE, (2008) The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nat Rev Genet 9: 699-712.
58. Farlow A, Meduri E, Dolezal M, Hua L, Schlotterer C, (2010) Nonsense-mediated decay enables intron gain in Drosophila. PLoS Genet 6: e1000819.
59. Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE, (2004) Analysis of segmental duplications and genome assembly in the mouse. Genome Res 14: 789-801.
60. Katju V, Lynch M, (2003) The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 165: 1793-1803.
61. She X, Jiang Z, Clark RA, Liu G, Cheng Z, et al. (2004) Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431: 927-930.
62. Lynch M, Conery JS, (2003) The evolutionary demography of duplicate genes. J Struct Funct Genomics 3: 35-44.
63. Tayebi N, Stubblefield BK, Park JK, Orvisky E, Walker JM, et al. (2003) Reciprocal and nonreciprocal recombination at the glucocerebrosidase gene region: implications for complexity in Gaucher disease. Am J Hum Genet 72: 519-534.
64. Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, et al. (2006) Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum Mutat 27: 545-552.
65. Casola C, Zekonyte U, Phillips AD, Cooper DN, Hahn MW, (2011) Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease. Genome Res.
66. Koch AL, (1972) Enzyme evolution. I. The importance of untranslatable intermediates. Genetics 72: 297-316.
67. Walsh JB, (1987) Sequence-dependent gene conversion: can duplicated genes diverge fast enough to escape conversion? Genetics 117: 543-557.
68. Marshall CR, Raff EC, Raff RA, (1994) Dollo's law and the death and resurrection of genes. Proc Natl Acad Sci U S A 91: 12283-12287.
69. Nei M, (2005) Selectionism and neutralism in molecular evolution. Mol Biol Evol 22: 2318-2342.
70. Nei M, (2007) The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A 104: 12235-12242.
71. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol.
72. Coggan M, Whitbread L, Whittington A, Board P, (1998) Structure and organization of the human theta-class glutathione S-transferase and D-dopachrome tautomerase gene complex. Biochem J 334 (Pt 3): 617-623.