Bibliography on gene and genome duplication (2003)

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  1. R Aburomia, O Khaner, A Sidow (2003), "Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail", Journal of Structural and Functional Genomics, 3:45-52.

  2. Keith L Adams, Richard Cronn, Ryan Percifield, Jonathan F Wendel (2003), "Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing", Proceedings of National Academy of Sciences, 100(8):4649-4654.

  3. Eduard D Akhunov, Andrew W Goodyear, Shu Geng, Li-Li Qi, Benjamin Echalier, Bikram S Gill, Miftahudin, J Perry Gustafson, Gerard Lazo, Shiaoman Chao, Olin D Anderson, Anna M Linkiewicz, Jorge Dubcovsky, Mauricio La Rota, Mark E Sorrells, Deshui Zhang7, Henry T Nguyen, Venugopal Kalavacharla, Khwaja Hossain, Shahryar F Kianian, Junhua Peng, Nora LV Lapitan, Jose L Gonzalez-Hernandez, James A Anderson, Dong-Woog Choi, Timothy J Close, Muharrem Dilbirligi, Kulvinder S Gill, M Kay Walker-Simmons, Camille Steber, Patrick E McGuire, Calvin O Qualset and Jan Dvorak (2003), "The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms", Genome Research, 13:753-763.
    [abstract]

  4. JA Bailey, EE Eichler (2003), "Genome-wide detection and analysis of recent segmental duplications within mammalian organisms", Cold Spring Harbor Symposium on Quantitative Biology, 68:115-124.

  5. JA Bailey, G Liu, EE Eichler (2003), "An alu transposition model for the origin and expansion of human segmental duplications", American Journal of Human Genetics, 73(4):823-834.
    abstract: Relative to genomes of other sequenced organisms, the human genome appears particularly enriched for large, highly homologous segmental duplications (90% sequence identity and 10 kbp in length). The molecular basis for this enrichment is unknown. We sought to gain insight into the mechanism of origin, by systematically examining sequence features at the junctions of duplications. We analyzed 9,464 junctions within regions of high-quality finished sequence from a genomewide set of 2,366 duplication alignments. We observed a highly significant (P < .0001) enrichment of Alu short interspersed element (SINE) sequences near or within the junction. Twenty-seven percent of all segmental duplications terminated within an Alu repeat. The Alu junction enrichment was most pronounced for interspersed segmental duplications separated by 1 Mb of intervening sequence. Alu elements at the junctions showed higher levels of divergence, consistent with Alu-Alumediated recombination events. When we classified Alu elements into major subfamilies, younger elements (AluY and AluS) accounted for the enrichment, whereas the oldest primate family (AluJ) showed no enrichment. We propose that the primate-specific burst of Alu retroposition activity (which occurred 3540 million years ago) sensitized the ancestral human genome for Alu-Alumediated recombination events, which, in turn, initiated the expansion of gene-rich segmental duplications and their subsequent role in nonallelic homologous recombination.

  6. JP Bielawski, Z Yang (2003), "Maximum likelihood methods for detecting adaptive evolution after gene duplication", Journal of Structural and Functional Genomics, 3:201-212.

  7. JE Bowers, BA Chapman, JK Rong, AH Paterson (2003), "Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events", Nature, 422:433-438.

  8. J Brosius (2003), "Gene duplication and other evolutionary strategies: from the RNA world to the future", Journal of Structural and Functional Genomics, 3:1-17.

  9. C Brun, A Guénoche, B Jacq (2003), "Approach of the functional evolution of duplicated genes in Saccharomyces cerevisiae using a new classification method based on protein-protein interaction data", Journal of Structural and Functional Genomics, 3:213-224.

  10. A Cavalcanti, R Ferreira, Z Gu, WH Li (2003), "Patterns of Gene Duplication in Yeast and C. elegans", Journal of Molecular Evolution, 56:28-37.

  11. Joseph Cheung, Xavier Estivill, Razi Khaja, Jeffrey R MacDonald, Ken Lau, Lap-Chee Tsui and Stephen W Scherer (2003), "Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence", Genome Biology, 4(4):R25.

  12. Joseph Cheung, Michael D Wilson, Junjun Zhang, Razi Khaja, Jeffrey R MacDonald, Henry HQ Heng, Ben F Koop, Stephen W Scherer (2003), "Recent segmental and gene duplications in the mouse genome", Genome Biology, 4:R47.
    [html]

  13. Gavin C. Conant, Andreas Wagner (2003), "Asymmetric sequence divergence of duplicate genes", Genome Research, 13:2052-2058.
    [abstract]

  14. William A Cresko, Yi-Lin Yan, David A Baltrus, Angel Amores, Amy Singer, Adriana Rodríguez-Marí, John H Postlethwait (2003), "Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish", Developmental Dynamics, 228(3):480-489.
    [ abstract]

  15. EGJ Danchin, L Abi-Rached, A Gilles, P Pontarotti (2003), "Conservation of the MHC-like region throughout evolution", Immunogenetics, 55(3):141-148.

  16. Lior David, Shula Blum, Marcus W Feldman, Uri Lavi, Jossi Hillel (2003), "Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci" Molecular Biology and Evolution, 20(9):1425-1434.
    [abstract]

  17. CI Davis-Castillo, DL Hartl (2003), "Conservation, relocation and duplication in genome evolution", Trends in Genetics, 19:593-597.

  18. D Durand (2003), "Vertebrate evolution: doubling and shuffling with a full deck", Trends in Genetics, 19(1):2-5.
    [PDF]

  19. Evan E Eichler, David Sankoff (2003), "Structural Dynamics of Eukaryotic Chromosome Evolution", Science, 301(5634):793-797.
    [ abstract]

  20. N El-Mabrouk, D Sankoff (2003), "The reconstruction of doubled genomes", SIAM Journal on Computing, 32(1):754-792.
    [ abstract]

  21. Maria D. Ermolaeva, Martin Wu, onathan A. Eisen, Steven L. Salzberg (2003), "The age of the Arabidopsis thaliana genome duplication", Plant Molecular Biology, 51(6):859-866.
    [ abstract]

  22. HE García, V Laudet, M Robinson-Rechavi (2003), "Nuclear receptors are markers of animal genome evolution", Journal of Structural and Functional Genomics, 3:177-184.

  23. X Gu (2003), "Evolution of duplicate genes versus genetic robustness against null mutations", Trends in Genetics, 19:354-356.

  24. X Gu (2003), "Functional divergence in protein (family) sequence evolution", Genetica, 118:133-141.

  25. Z Gu, LM Steinmetz, X Gu, C Scharfe, RW Davis, WH Li (2003), "Role of duplicate genes in genetic robustness against null mutations", Nature, 421:63-66.
    [PDF]

  26. K Hokamp, A McLysaght, KH Wolfe (2003), "The 2R hypothesis and the human genome sequence", Journal of Structural and Functional Genomics, 3:95-110.

  27. PWH Holland (2003), "More genes in vertebrates?", Journal of Structural and Functional Genomics, 3:75-84.

  28. Edward Hollox, John AL Armour, JCK Barber (2003), "Extensive normal copy number variation of a b-defensin antimicrobial-gene cluster", American Journal of Human Genetics, 73:591-600.

  29. Sean D Hooper, Otto G Berg (2003), "On the nature of gene innovation: duplication patterns in microbial genomes", Molecular Biology and Evolution, 20:945-954.
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  30. Sean D Hooper, Otto G Berg (2003), "Duplication is more common among laterally transferred genes than among indigenous genes", Genome Biology, 4:R48.
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  31. Amy C Horton, Navin R Mahadevan, Ilya Ruvinsky, Jeremy J Gibson-Brown (2003), "Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution", Journal of Experimental Zoology B: Molecular and Development Evolution, 299(1):4-53.1
    [ abstract]

  32. Li-Cheng Hsieh, Liaofu Luo, Hoong-Chien Lee (2003), "Short segmental duplication: parsimony in growth of microbial genomes", Genome Biology, 4:P7. (preprint)

  33. LV Hua, K Hidaka, X Pesesse, LD Barnes, SB Shears (2003), "Paralogous murine Nudt10 and Nudt11 genes have differential expression patterns but encode identical proteins that are physiologically competent diphosphoinositol polyphosphate phosphohydrolases", Biochmical Journal, 373:81-89.

  34. AL Hughes, R Friedman (2003), "2R or not 2R: Testing hypotheses of genome duplication in early vertebrates", Journal of Structural and Functional Genomics, 3:85-93.

  35. C Jozefowicz, J McClintock, V Prince (2003), "The fates of zebrafish Hox gene duplicates", Journal of Structural and Functional Genomics, 3:185-194.

  36. Vaishali Katjua, Michael Lynch (2003), "The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans Genome", Genetics, 165:1793-1803.

  37. W James Kent, Robert Baertsch, Angie Hinrichs, Webb Miller, David Haussler (2003), "Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes", Proceedings of National Academy of Sciences, 100(20):11484-11489.
    [ abstract]

  38. CB Kim, CS Shashikant, K Sumiyama, WCH Wang, CT Amemiya, FH Ruddle (2003), "Phylogenetic analysis of the mammalian Hoxc8 non-coding region", Journal of Structural and Functional Genomics, 3:195-199.

  39. Elena M Kramer, Veronica S di Stilio, Philipp M Schluter (2003), "Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae", International Journal of Plant Science, 164(1):1-11.

  40. A Lecharny, N Boudet, I Gy, S Aubourg, M Kreis (2003), "Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure", Journal of Structural and Functional Genomics, 3:111-116.

  41. S Le Crom, M Kapsimali, PO Barme, P Vernier (2003), "Dopamine receptors for every species: Gene duplications and functional diversification in Craniates", Journal of Structural and Functional Genomics, 3:161-176.

  42. RB Langkjaer, PF Cliften, M Johnson, J Piskur (2003), "Yeast genome duplication was followed by asynchronous differentiation of duplicated genes", Nature, 421:848-852.
    Abstract: Gene redundancy has been observed in yeast, plant and human genomes, and is thought to be a consequence of whole-genome duplications. Baker's yeast, Saccharomyces cerevisiae, contains several hundred duplicated genes. Duplication(s) could have occurred before or after a given speciation. To understand the evolution of the yeast genome, we analysed orthologues of some of these genes in several related yeast species. On the basis of the inferred phylogeny of each set of genes, we were able to deduce whether the gene duplicated and/or specialized before or after the divergence of two yeast lineages. Here we show that the gene duplications might have occurred as a single event, and that it probably took place before the Saccharomyces and Kluyveromyces lineages diverged from each other. Further evolution of each duplicated gene pair-such as specialization or differentiation of the two copies, or deletion of a single copy--has taken place independently throughout the evolution of these species.

  43. Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, François Coulier (2003), "ParaDB: a tool for paralogy mapping in vertebrate genomes", Nucleic Acids Research, 31:63-67.
    [html]

  44. WH Li, Z Gu, AO Cavalcanti, A Nekrutenko (2003), "Detection of gene duplications and block duplications in eukaryotic genomes", Journal of Structural and Functional Genomics, 3:27-34.

  45. Bao Liu, Jonathan F. Wendel (2003), "Epigenetic phenomena and the evolution of plant allopolyploids", Molecular Phylogenetics and Evolution, 29(3):365-379.
    [ abstract]

  46. DP Locke, N Archidiacono, D Misceo, MF Cardone, S Deschamps, B Roe, M Rocchi, EE Eichler (2003), "Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster", Genome Biology, 4:R50.
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  47. M Long, E Betran, K Thornton, W Wang (2003), "The origin of new genes:glimpses from the young and old", Nature Reviews Genetics, 4:865-875.

  48. M Long, M Deutsch, W Wang, E Betrán, F Brunet, J Zhang (2003), "Origin of new genes: results from experimental and computational analysis", Genetica, 118:171-182.

  49. LG Lundin, D Larhammar, F Hallböök (2003), "Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates", Journal of Structural and Functional Genomics, 3:53-63.
    abstract: The appearance of the vertebrates demarcates some of the most far-reaching changes of structure and function seen during the evolution of the metazoans. These drastic changes of body plan and expansion of the central nervous system among other organs coincide with increased gene numbers. The presence of several groups of paralogous chromosomal regions in the human genome is a reflection of this increase. The simplest explanation for the existence of these paralogies would be two genome doublings with subsequent silencing of many genes. It is argued that gene localization data and the delineation of paralogous chromosomal regions give more reliable information about these types of events than dendrograms of gene families as gene relationships are often obscured by uneven replacement rates as well as other factors. Furthermore, the topographical relations of some paralogy groups are discussed.

  50. M Lynch, JS Conery (2003), "The origin of genome complexity", Science, 302:1401-1404.

  51. M Lynch, JS Conery (2003), "The evolutionary demography of duplicate genes", Journal of Structural and Functional Genomics, 3:35-44.

  52. A Meyer (2003), "Duplication, duplication" (news and views), Nature, 421:31-32.
    [PDF]

  53. edited, Axel Meyer, Yves van de Peer (2003), Genome Evolution: Gene and Genome Duplication and the Origin of Novel Gene Functions (Springer). ISBN: 1402010214.

  54. A Meyer, Y van de Peer (2003), "'Natural selection merely modified while redudancy created' -- Susumu Ohno's idea of evolutionary importance of gene and genome duplication", Journal of Structural and Functional Genomics, 3:vii-ix.
    [PDF]

  55. Richard C Moore, Michael D Purugganan (2003), "The early stages of duplicate gene evolution", Proceedings of National Academy of Sciences, 100(26):15682-15687.
    [abstract]

  56. Thomas C Osborn, J Chris Pires, James A Birchler, Donald L Auger, Z Jeffery Chen, Hyeon-Se Lee, Luca Comai, Andreas Madlung, R W Doerge, Vincent Colot, Robert A Martienssen (2003), "Understanding mechanisms of novel gene expression in polyploids", Trends in Genetics, 19(3):141-147.
    [ abstract]

  57. Georgia Panopoulou, Steffen Hennig, Detlef Groth, Antje Krause, Albert J Poustka, Ralf Herwig, Martin Vingron, Hans Lehrach (2003), "New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes", Genome Research, 13:1056-1066.
    [abstract]

  58. B Papp, C Pal, LD Hurst (2003), "Evolution of cis-regulatory elements in duplicated genes of yeast", Trends in Genetics, 19:417-422.

  59. IA Parkin, AG Sharpe, DJ Lydiate (2003), "Patterns of genome duplication within the Brassica napus genome", Genome, 46(2):291-303.

  60. Romualdo Pastor-Satorras, Eric Smith, Ricard V Sole (2003), "Evolving protein interaction networks through gene duplication", Journal of Theoretical Biology, 222(2):199-210.
    [ abstract]

  61. J Piatigorsky (2003), "Crystallin genes: specialization by changes in gene regulation may precede gene duplication", Journal of Structural and Functional Genomics, 3:131-137.

  62. Jeroen Raes, Yves Van de Peer (2003), "Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico", Applied Bioinformatics, 2(2):91-101.
    [ abstract]

  63. J Raes, K Vandepoele, Y Saeys, C Simillion, Y Van de Peer (2003), "Investigating ancient duplication events in the Arabidopsis genome", Journal of Structural and Functional Genomics, 3:117-129.

  64. SN Rodin, AD Riggs (2003), "Epigenetic silencing may aid evolution by gene duplication", Journal of Molecular Evolution, 56(6):718-729.

  65. E Salaneck, D H Ardell, E T Larson, D Larhammar (2003), "Three neuropeptide Y receptor genes in the spiny dogfish, squalus acanthias, support en bloc duplications in early vertebrate evolution", Molecular Biology and Evolution, 20(8):1271-1280.
    [abstract]

  66. Cathal Seoighe (2003), "Turning the clock back on ancient genome duplication", Current Opinion in Genetics and Development, 13:636-643.
    [PDF]

  67. C Seoighe C, CR Johnston, DC Shields (2003), "Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation", Molecular Biology and Evolution, 20(4):484-490.

  68. DE Soltis, PS Soltis, MD Bennett, IJ Leitch (2003), "Evolution of genome size in the angiosperms", American Journal of Botany, 90(11):1596-1603.

  69. J Spring (2003), "Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates", Journal of Structural and Functional Genomics, 3:19-25.

  70. K Sumiyama, SQ Irvine, FH Ruddle (2003), "The role of gene duplication in the evolution and function of the vertebrate Dlx/distal-less bigene clusters", Journal of Structural and Functional Genomics, 3:151-159.

  71. JS Taylor, I Braasch, T Frickey, A Meyer, Y van de Peer (2003), "Genome duplication, a trait shared by 22,000 species of ray-finned fish", Genome Research, 13:382-390.
    [abstract]

  72. Y van de Peer, JS Taylor, A Meyer (2003), "Are all fishes ancient polyploids?" Journal of Structural and Functional Genomics, 3:65-73.

  73. K Vandepoele, C Simillion, Y van de Peer (2003), "Evidence that rice and other cereals are ancient aneuploids", Plant Cell, 15:2192-2202.
    [abstract]

  74. A Vienne, J Rasmussen, L Abi-Rached, P Pontarotti, A Gilles (2003), "Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region", Molecular Biology and Evolution, 20(8):1290-1298.

  75. JN Volff, M Schartl (2003), "Evolution of signal transduction by gene and genome duplication in fish", Journal of Structural and Functional Genomics, 3:139-150.

  76. J Zhang (2003), "Evolution by gene duplication: an update", Trends in Ecology and Evolution,18:292-298.
    [PDF]

  77. Louxin Zhang , Bin Ma, Lusheng Wang, Ying Xu (2003), "Greedy method for inferring tandem duplication history", Bioinformatics, 19:1497-1504.

  78. P Zhang, Z Gu, WH Li (2003), "Different evolutionary patterns between young duplicate genes in the human genome", Genome Biology, 4:R56.