gene duplication

Summary

Summary: Processes occurring in various organisms by which new genes arise, i.e. the duplication of a single gene. In contiguous gene duplication, the duplicated sequence coexists within the boundaries set by the start and stop signals for protein synthesis of the original, resulting in a larger transcription product and protein at the expense of the preexisting protein. In discrete gene duplication, the duplicated sequence is outside the start and stop signals, resulting in two independent genes (GENES, DUPLICATE) and gene products. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

Top Publications

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  2. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
  3. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
  4. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
  5. pmc The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
  6. ncbi The evolution of gene duplications: classifying and distinguishing between models
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Nat Rev Genet 11:97-108. 2010
  7. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
  8. pmc Preservation of duplicate genes by complementary, degenerative mutations
    A Force
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 151:1531-45. 1999
  9. pmc The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana
    Steven B Cannon
    Plant Biology Department, University of Minnesota, St, Paul, MN 55108, USA
    BMC Plant Biol 4:10. 2004
  10. ncbi The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003

Detail Information

Publications287 found, 100 shown here

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  2. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
    ..All data are made available in a number of formats and will be kept up to date with the Ensembl project...
  3. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
    ..About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance...
  4. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    b>Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions...
  5. pmc The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
    ..The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters...
  6. ncbi The evolution of gene duplications: classifying and distinguishing between models
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Nat Rev Genet 11:97-108. 2010
    ..Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications...
  7. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in ..
  8. pmc Preservation of duplicate genes by complementary, degenerative mutations
    A Force
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 151:1531-45. 1999
    ..is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually ..
  9. pmc The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana
    Steven B Cannon
    Plant Biology Department, University of Minnesota, St, Paul, MN 55108, USA
    BMC Plant Biol 4:10. 2004
    ....
  10. ncbi The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  11. ncbi Synteny and collinearity in plant genomes
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Science 320:486-8. 2008
    ..Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character...
  12. ncbi The evolutionary significance of ancient genome duplications
    Yves Van de Peer
    Department of Plant Systems Biology, VIB Flanders Institute of Biotechnology, Ghent, Belgium
    Nat Rev Genet 10:725-32. 2009
    ....
  13. pmc Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms
    Yupeng Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 6:e28150. 2011
    ..However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored.
  14. pmc Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 18:1944-54. 2008
    ..Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes...
  15. pmc Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
    Todd J Treangen
    Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
    PLoS Genet 7:e1001284. 2011
    b>Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes...
  16. ncbi The sequence of the human genome
    J C Venter
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 291:1304-51. 2001
    ..Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge...
  17. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
    ..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
  18. ncbi Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Annu Rev Plant Biol 60:433-53. 2009
    Each mode of gene duplication (tandem, tetraploid, segmental, transpositional) retains genes in a biased manner...
  19. pmc Comparative analysis of the receptor-like kinase family in Arabidopsis and rice
    Shin Han Shiu
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Plant Cell 16:1220-34. 2004
    ..These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes...
  20. ncbi The amphioxus genome and the evolution of the chordate karyotype
    Nicholas H Putnam
    Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 453:1064-71. 2008
    ..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...
  21. pmc A genome triplication associated with early diversification of the core eudicots
    Yuannian Jiao
    Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 13:R3. 2012
    ..Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear...
  22. ncbi Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish
    Simone Hoegg
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    J Mol Evol 59:190-203. 2004
    ..The additional number of genes resulting from this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish...
  23. ncbi Gene duplication and evolutionary novelty in plants
    Lex E Flagel
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    New Phytol 183:557-64. 2009
    ..This has led many researchers to speculate that gene duplication may have played an important role in the evolution of phenotypic novelty within plants...
  24. ncbi Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster
    J J Emerson
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Science 320:1629-31. 2008
    ..Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection...
  25. pmc Evolution at two levels: on genes and form
    Sean B Carroll
    Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, Madison, Wisconsin, USA
    PLoS Biol 3:e245. 2005
  26. pmc Strong association of de novo copy number mutations with autism
    Jonathan Sebat
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 316:445-9. 2007
    ..Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized...
  27. ncbi A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
    Jennifer A Lee
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, 77030, USA
    Cell 131:1235-47. 2007
    ..We propose that complex duplication and deletion rearrangements associated with PMD, and potentially other nonrecurrent rearrangements, may be explained by this replication-based mechanism...
  28. ncbi The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
    Science 319:64-9. 2008
    ..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
  29. ncbi Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    Olivier Jaillon
    UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Nature 431:946-57. 2004
    ....
  30. pmc The role of nucleosome positioning in the evolution of gene regulation
    Alexander M Tsankov
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Biol 8:e1000414. 2010
    ..Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation...
  31. pmc Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula
    Carine Ameline-Torregrosa
    Laboratoire des Interactions Plantes Microorganismes, UMR CNRS INRA 442 2594, 31326, Castanet Tolosan, France
    Plant Physiol 146:5-21. 2008
    ..This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome...
  32. pmc Adaptive evolution of young gene duplicates in mammals
    Mira V Han
    School of Informatics, Indiana University, Bloomington, IN 47405, USA
    Genome Res 19:859-67. 2009
    ..The results are also in agreement with the classical model of evolution by gene duplication, supporting a common role for neofunctionalization in the long-term maintenance of gene duplicates.
  33. ncbi Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes
    J L Riechmann
    Mendel Biotechnology, 21375 Cabot Boulevard, Hayward, CA 94545, USA
    Science 290:2105-10. 2000
    ..The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription...
  34. ncbi The origins of genome complexity
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 302:1401-4. 2003
    ..The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies...
  35. ncbi Yesterday's polyploids and the mystery of diploidization
    K H Wolfe
    Department of Genetics, Smurfit Institute, Trinity College, University of Dublin, Dublin 2, Republic of Ireland
    Nat Rev Genet 2:333-41. 2001
    ..The greatest mystery is the molecular basis of diploidization, the evolutionary process by which a polyploid genome turns into a diploid one...
  36. pmc Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
    Frédéric Choulet
    Institut National de la Recherche Agronomique, Universite Blaise Pascal, Unité Mixte de Recherche 1095 Genetics Diversity and Ecophysiology of Cereals, F 63100 Clermont Ferrand, France
    Plant Cell 22:1686-701. 2010
    ....
  37. ncbi Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 422:433-8. 2003
    ....
  38. ncbi Gene duplication and the evolution of plant MADS-box transcription factors
    Chiara A Airoldi
    Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
    J Genet Genomics 39:157-65. 2012
    ....
  39. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    Stephen A Goff
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Science 296:92-100. 2002
    ..Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops...
  40. ncbi Autoreactive B cell responses to RNA-related antigens due to TLR7 gene duplication
    Prapaporn Pisitkun
    Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases NIAID, NIH, Rockville, MD 20852, USA
    Science 312:1669-72. 2006
    ..These results reveal high divergence in mouse Y chromosomes and represent a good example of gene copy number qualitatively altering a polygenic disease manifestation...
  41. ncbi Gene duplication and the adaptive evolution of a classic genetic switch
    Chris Todd Hittinger
    Howard Hughes Medical Institute, Laboratory of Genetics, University of Wisconsin Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA
    Nature 449:677-81. 2007
    How gene duplication and divergence contribute to genetic novelty and adaptation has been of intense interest, but experimental evidence has been limited...
  42. pmc Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
    Guillaume Blanc
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, 2, Ireland
    Plant Cell 16:1667-78. 2004
    ..in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat [Triticum aestivum], maize [Zea mays], tetraploid cotton [..
  43. pmc Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
    Jeffrey A Fawcett
    Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium
    Proc Natl Acad Sci U S A 106:5737-42. 2009
    ....
  44. pmc Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes
    Melissa D Lehti-Shiu
    Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
    Plant Physiol 150:12-26. 2009
    ..Finally, we propose that the detection of highly variable molecular patterns associated with specific pathogens/parasites is the main reason for the up-regulation of hundreds of RLK/Pelles under biotic stress...
  45. pmc High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications
    Tamim H Shaikh
    Division of Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
    Genome Res 19:1682-90. 2009
    ..Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics...
  46. ncbi Lateral transfer of genes from fungi underlies carotenoid production in aphids
    Nancy A Moran
    Department of Ecology and Evolutionary Biology, 1041 East Lowell Street, University of Arizona, Tucson, AZ 85721, USA
    Science 328:624-7. 2010
    ..A mutation causing an amino acid replacement in this desaturase results in loss of torulene and of red body color. Thus, aphids are animals that make their own carotenoids...
  47. pmc The genome of the social amoeba Dictyostelium discoideum
    L Eichinger
    Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph Stelzmann Str 52, 50931 Cologne, Germany
    Nature 435:43-57. 2005
    ....
  48. ncbi Distinguishing among evolutionary models for the maintenance of gene duplicates
    Matthew W Hahn
    Department of Biology and School of Informatics, Indiana University, Bloomington, IN 47405, USA
    J Hered 100:605-17. 2009
    ..Though the various outcomes of gene duplication are often strictly associated with the presence or absence of adaptive natural selection, I argue that ..
  49. ncbi Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene
    Dario Leister
    Abteilung für Pflanzezüchtung und Ertragsphysiologie, Max Planck Instutut für Züchtungsforschung, Koln, Germany
    Trends Genet 20:116-22. 2004
    ..Once physically removed from their closest relatives, the NBS-LRR genes might adopt and preserve new specificities because they are less prone to sequence homogenization...
  50. pmc Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium)
    Bhupendra Chaudhary
    Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
    Genetics 182:503-17. 2009
    ..These results provide a novel temporal perspective on expression evolution of duplicate genomes and add to our understanding of the importance of polyploidy in plants...
  51. ncbi Turning a hobby into a job: how duplicated genes find new functions
    Gavin C Conant
    Division of Animal Sciences, University of Missouri Columbia, 163B Animal Sciences Center, 920 East Campus Drive, Columbia, Missouri 65211 5300, USA
    Nat Rev Genet 9:938-50. 2008
    b>Gene duplication provides raw material for functional innovation...
  52. pmc Ohno's dilemma: evolution of new genes under continuous selection
    Ulfar Bergthorsson
    Department of Biology, University of New Mexico, Albuquerque, NM 87131 0001, USA
    Proc Natl Acad Sci U S A 104:17004-9. 2007
    ..Improvement of some copies relaxes selection on others and allows their loss by mutation (becoming pseudogenes). Ultimately one of the extra copies is able to provide all of the new activity...
  53. pmc Gene duplication as a mechanism of genomic adaptation to a changing environment
    Fyodor A Kondrashov
    Institucio Catalana de Recerca i Estudis Avancats, Centre for Genomic Regulation CRG and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain
    Proc Biol Sci 279:5048-57. 2012
    ....
  54. pmc Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication
    Alireza Eshaghi
    Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
    PLoS ONE 7:e32807. 2012
    ..The 23 amino acid ON1 G gene duplication results in a repeat of 7 potential O-glycosylation sites including three O-linked sugar acceptors at residues ..
  55. ncbi The flowering world: a tale of duplications
    Yves Van de Peer
    Department of Plant Systems Biology, Flanders Institute for Biotechnology VIB, 9052 Gent, Belgium
    Trends Plant Sci 14:680-8. 2009
    ..This is important if we want to demonstrate the significance of genome duplications for the evolution and radiation of (different groups of) flowering plants...
  56. pmc Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 107:472-7. 2010
    ..Although the exact timing of the sigma-duplication(s) is unclear because of uncertainties of the molecular clock assumption, our data suggest that it occurred early in the monocot lineage after its divergence from the eudicot clade...
  57. ncbi The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:951-63. 2008
    ..it has become clear that a substantial portion is generated by genomic drift, a random process of gene duplication and deletion...
  58. ncbi Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?
    Shigehiro Kuraku
    Laboratory for Evolutionary Morphology, RIKEN Center for Developmental Biology, Kobe, Japan
    Mol Biol Evol 26:47-59. 2009
    ..Apart from subsequent lineage-specific modifications, these ancient genome duplication events might serve generally to distinguish vertebrates from invertebrates at the genomic level...
  59. pmc Evolution of pigment synthesis pathways by gene and genome duplication in fish
    Ingo Braasch
    University of Wurzburg, Physiological Chemistry I, Biozentrum, Am Hubland, Wurzburg, Germany
    BMC Evol Biol 7:74. 2007
    ..No systematic genomic inventory allowing to test this hypothesis has been drawn up so far for pigmentation genes in fish, and almost nothing is known about the evolution of these genes in different fish lineages...
  60. pmc MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress
    Rita Arora
    Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
    BMC Genomics 8:242. 2007
    ....
  61. ncbi A hybrid micro-macroevolutionary approach to gene tree reconstruction
    Dannie Durand
    Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
    J Comput Biol 13:320-35. 2006
    ..g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction ..
  62. pmc RNA-based gene duplication: mechanistic and evolutionary insights
    Henrik Kaessmann
    Center for Integrative Genomics, University of Lausanne, Genopode, CH 1015 Lausanne, Switzerland
    Nat Rev Genet 10:19-31. 2009
    ..For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes.
  63. pmc Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world
    Lucie Parenicová
    Dipartimento di Biologia, Universitá degli Studi di Milano, 20133 Milan, Italy
    Plant Cell 15:1538-51. 2003
    ..MADS-box genes also constitute an excellent system with which to study the evolution of complex gene families in higher plants...
  64. pmc Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli
    Kousuke Hanada
    Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
    Plant Physiol 148:993-1003. 2008
    Plants have substantially higher gene duplication rates compared with most other eukaryotes. These plant gene duplicates are mostly derived from whole genome and/or tandem duplications...
  65. ncbi Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    Manolis Kellis
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 428:617-24. 2004
    ..Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions...
  66. ncbi A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
    ..Limitations of the new method are discussed...
  67. pmc Sequencing of natural strains of Arabidopsis thaliana with short reads
    Stephan Ossowski
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Genome Res 18:2024-33. 2008
    ..Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org...
  68. pmc Duplication hotspots, rare genomic disorders, and common disease
    Heather C Mefford
    Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
    Curr Opin Genet Dev 19:196-204. 2009
    ..The genomic hotspot model may provide a powerful approach for understanding the role of rare variants in common disease...
  69. ncbi How confident can we be that orthologs are similar, but paralogs differ?
    Romain A Studer
    Department of Ecology and Evolution, Biophore, Lausanne University, CH 1015 Lausanne, Switzerland and Swiss Institute of Bioinformatics, CH 1015 Lausanne, Switzerland
    Trends Genet 25:210-6. 2009
    ..Thus, functional change between orthologs might be as common as between paralogs, and future studies should be designed to test the impact of duplication against this alternative model...
  70. pmc Gene duplication and fragmentation in the zebra finch major histocompatibility complex
    Christopher N Balakrishnan
    Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
    BMC Biol 8:29. 2010
    ....
  71. pmc Maintenance of duplicate genes and their functional redundancy by reduced expression
    Wenfeng Qian
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Trends Genet 26:425-30. 2010
    ..Whereas the majority of the expression reductions are likely to be neutral, some are apparently beneficial to rebalancing gene dosage after duplication...
  72. ncbi A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit
    Han Xiao
    Department of Horticulture and Crop Science, Ohio State University Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA
    Science 319:1527-30. 2008
    ..We show that the locus arose as a result of an unusual 24.7-kilobase gene duplication event mediated by the long terminal repeat retrotransposon Rider...
  73. pmc Automated identification of conserved synteny after whole-genome duplication
    Julian M Catchen
    Department of Computer and Information Science, University of Oregon, Eugene, Oregon 97403, USA
    Genome Res 19:1497-505. 2009
    ..To demonstrate the utility of the system, we present a case study of gene family evolution, investigating the ARNTL gene family in the genomes of Ciona intestinalis, amphioxus, zebrafish, and human...
  74. ncbi A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse
    Gerli Rosengren Pielberg
    Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE 751 24 Uppsala, Sweden
    Nat Genet 40:1004-9. 2008
    ..The Gray horse provides a notable example of how humans have cherry-picked mutations with favorable phenotypic effects in domestic animals...
  75. pmc A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish
    Lieke M van der Aa
    Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Jouy en Josas, France
    BMC Biol 7:7. 2009
    ..Accordingly, antiviral TRIMs have diversified highly through gene expansion, positive selection and alternative splicing. Characterizing immune TRIMs in other vertebrates may enlighten their complex evolution...
  76. pmc Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity
    Daniel Lang
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
    Genome Biol Evol 2:488-503. 2010
    ..Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity...
  77. ncbi Arrangements in the modular evolution of proteins
    Andrew D Moore
    Evolutionary Bioinformatics, IEB, University of Munster, Hüfferstrasse 1, Munster, Germany
    Trends Biochem Sci 33:444-51. 2008
    ..Although some mechanisms that govern modular rearrangements of protein domains have been uncovered, such as the addition or deletion of a single N- or C-terminal domain, much is still unknown about the genetics behind these arrangements...
  78. ncbi Journey through the past: 150 million years of plant genome evolution
    Sebastian Proost
    Department of Plant Systems Biology, VIB, Technologiepark 927, B 9052 Ghent, Belgium
    Plant J 66:58-65. 2011
    ..thaliana genome, covering about 150 million years of evolution characterized by gene and genome duplications, genome rearrangements and genome reduction...
  79. pmc Birth and death of genes linked to chromosomal inversion
    Yoshikazu Furuta
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Proc Natl Acad Sci U S A 108:1501-6. 2011
    ..These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells...
  80. ncbi Genome evolution in yeasts
    Bernard Dujon
    Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
    Nature 430:35-44. 2004
    ....
  81. ncbi Large-scale copy number polymorphism in the human genome
    Jonathan Sebat
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Science 305:525-8. 2004
    ..We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease...
  82. pmc Origins of recently gained introns in Caenorhabditis
    Avril Coghlan
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Proc Natl Acad Sci U S A 101:11362-7. 2004
    ..All of these similarities involve minisatellites or palindromes in the intron sequences. Our results suggest that at least some of the intron gains were caused by reverse splicing of a preexisting intron...
  83. pmc Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence
    Wan Kyu Kim
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS Comput Biol 4:e1000232. 2008
    ..Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these ..
  84. pmc Taxonomically restricted genes are associated with the evolution of sociality in the honey bee
    Brian R Johnson
    Department of Environmental Science, Policy and Management University of California, Berkeley 137 Mulford Hall, MC3114 Berkeley, CA 94720 3114 USA
    BMC Genomics 12:164. 2011
    ..The genetic basis of this expansion in behavioral repertoire is still poorly understood, and a role for taxonomically restricted genes has not been explored at the whole genome level...
  85. ncbi Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana
    David Bikard
    Genetics and Plant Breeding, INRA, SGAP UR254, F 78026 Versailles, France
    Science 323:623-6. 2009
    ..Our data suggest that these passive mechanisms, gene duplication and extinction, could represent an important source of genetic incompatibilities across all taxa.
  86. pmc Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication
    Angèle Tingaud-Sequeira
    Laboratory of Institut de Recerca i Tecnologia Agroalimentàries Institut de Ciències del Mar, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
    BMC Evol Biol 8:259. 2008
    ..However, teleosts have an additional AQP isoform structurally more similar to AQP1, though its relationship with AQP1o is unclear...
  87. ncbi DAGchainer: a tool for mining segmental genome duplications and synteny
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 20:3643-6. 2004
    ..Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer...
  88. pmc The probability of duplicate gene preservation by subfunctionalization
    M Lynch
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 154:459-73. 2000
    ....
  89. ncbi Automatic genome-wide reconstruction of phylogenetic gene trees
    Ilan Wapinski
    Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Bioinformatics 23:i549-58. 2007
    b>Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale are still in their infancy...
  90. ncbi Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
    H Tettelin
    The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 293:498-506. 2001
    ..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
  91. pmc The origins and impact of primate segmental duplications
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
    Trends Genet 25:443-54. 2009
    ..Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses...
  92. ncbi Gene co-option in physiological and morphological evolution
    John R True
    Department of Ecology and Evolution, State University of New York at Stony Brook, 11794 5245, USA
    Annu Rev Cell Dev Biol 18:53-80. 2002
    ..This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions...
  93. ncbi Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
    Jean Marc Aury
    Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
    Nature 444:171-8. 2006
    ..The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints...
  94. ncbi PLP1 gene duplication causes overexpression and alteration of the PLP/DM20 splicing balance in fibroblasts from Pelizaeus-Merzbacher disease patients
    Stefano Regis
    Laboratorio Diagnosi Pre Postnatale Malattie Metaboliche, Istituto G Gaslini, Largo G Gaslini 5, 16147 Genova, Italy
    Biochim Biophys Acta 1792:548-54. 2009
    ..expression, we analysed the PLP/DM20 expression profile in fibroblasts from three PMD patients with a PLP1 gene duplication. Gene expression was evaluated by real-time PCR using two different PLP1 amplicons and two different ..
  95. pmc Evolution by leaps: gene duplication in bacteria
    Margrethe H Serres
    Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Biol Direct 4:46. 2009
    ..The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution...
  96. ncbi Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia
    Idoya Lahortiga
    Human Genome Laboratory, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium
    Nat Genet 39:593-5. 2007
    ..Our results identify duplication of MYB as an oncogenic event and suggest that MYB could be a therapeutic target in human T-ALL...
  97. ncbi APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy
    Anne Rovelet-Lecrux
    Inserm U614 IFRMP, Faculty of Medicine, Rouen, France
    Nat Genet 38:24-6. 2006
    ..37 Mb. Brains from individuals with APP duplication showed abundant parenchymal and vascular deposits of amyloid-beta peptides. Duplication of the APP locus, resulting in accumulation of amyloid-beta peptides, causes ADEOAD with CAA...
  98. pmc Preferential regulation of duplicated genes by microRNAs in mammals
    Jingjing Li
    Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, ON, M5S 1A8, Canada
    Genome Biol 9:R132. 2008
    ..Specifically, while mammalian paralogs are known to overcome their initial complete functional redundancy through variation in regulation and expression, the potential involvement of microRNAs in this process has not been investigated...

Research Grants63

  1. Roles of the mammalian CST complex in DNA replication and chromosome cohesion
    JASON AARON STEWART; Fiscal Year: 2013
    ..lead to phenotypes associated with cancer initiation, such as translocations, deletions, chromosome fusions, gene duplication and aneuploidy...
  2. Phylogenomics and functional diversification of the Heterochromatin Protein 1 gen
    MIA TAUNA LEVINE; Fiscal Year: 2012
    ..My preliminary survey of the many uncharacterized HP1-derived gene duplication events across the human genome implicates similar, though unexplored, evolutionary dynamics consistent with ..
  3. Sexual conflict and relocation of genes by duplication
    ESTHER BETRAN; Fiscal Year: 2013
    ..applicant): The long-term objective of our research is to investigate the patterns that arise as a result of gene duplication to better understand the evolutionary forces that drive genome architecture...
  4. Identifying and characterizing gene(s) involved in beta-amyloid production.
    Huaxi Xu; Fiscal Year: 2013
    ..ribosomal protein S23) mRNA retroposition, a process where mRNA is reintegrated into the genome resulting in gene duplication/evolution...
  5. Site-directed RNA editing: a new method to correct disease causing mutations
    Joshua J C Rosenthal; Fiscal Year: 2013
    ..An example is Rett Syndrome, caused by mutations in the Mecp2 gene. Mecp2 gene duplication, as well as loss-of-function, results in severe disease...
  6. Molecular genetics of Pelizaeus-Merzbacher disease
    Grace M Hobson; Fiscal Year: 2013
    ..Motor milestones and speech are also delayed in most patients. Neither the molecular mechanisms of gene duplication nor the molecular basis for the clinical phenotype in PMD is well understood...
  7. Regulation of Substrate Binding and Catalysis in tRNase Z
    LOUIS F LEVINGER; Fiscal Year: 2010
    ..Aim 2] Because the long form of tRNase Z (tRNase ZL) is thought to have originated as a tandem gene duplication of the short form (tRNase ZS), an altered version of the motif I region (?-motif I) may be found toward the ..
  8. Functional genomic approaches to duplicate gene evolution
    Jianzhi Zhang; Fiscal Year: 2012
    ..b>Gene duplication is wildly regarded as the primary source of new genes, but the general patterns and mechanisms of functional ..
  9. The role of PON2 and PON3 proteins in Atherosclerosis
    Srinivasa Reddy; Fiscal Year: 2013
    ..Sequence analysis of PON genes suggest that the PON family evolved by gene duplication with PON2 being the first and PON1 the most recent member...
  10. Evolution of sex chromosome meiotic drive in stalk eyed fly populations
    Kimberly A Paczolt; Fiscal Year: 2013
    ..will be used to test the hypothesis that intragenomic conflict caused by meiotic drive has driven increased gene duplication and gene movement...
  11. Pathophysiology of APP in vivo
    Hui Zheng; Fiscal Year: 2013
    ..Mutations or gene duplication of APP are causal for a subset of early onset AD, establishing its central role in AD pathogenesis...
  12. Rewiring the yeast brain: Redundancy and interference in genetic networks
    NICOLAS EMILE BUCHLER; Fiscal Year: 2011
    ..b>Gene duplication followed by a loss-of-function mutation can generate a dominant-negative...
  13. Molecular and Structural Basis for T Cell Costimulation
    Stanley G Nathenson; Fiscal Year: 2012
    ..The genes for costimulatory molecules are often present as tightly linked loci formed by gene duplication events, and as a consequence the members within a given family of costimulatory molecules share common ..
  14. Methods for evolutionary analysis of eukaryotic transcriptional regulation
    Sridhar Hannenhalli; Fiscal Year: 2011
    ..b>Gene duplication is a major driver of evolutionary innovation, as it allows an organism to elaborate existing biological ..
  15. COMPARATIVE MOLECULAR SEQUENCE ANALYSIS
    Sudhir Kumar; Fiscal Year: 2013
    ..cross-platform, and implementing efficient heuristics for estimating very large trees quickly and inferring gene duplication events and divergence times...
  16. OZONE EFFECTS ON FUNCTION OF SURFACTANT PROTEIN VARIANTS
    Joanna Floros; Fiscal Year: 2010
    ..Knowledge gained may help explain and perhaps link the in vitro data with the human genetic association data, and provide insight in the understanding of the value of the SP-A gene duplication.
  17. Gene duplication in the evolution of novel phenotypes and human disease
    Raquel Assis; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Gene duplication is a key source of genetic novelty, which in the best case leads to the acquisition of advantageous phenotypes, and in the worst results in disease...
  18. Phylogenetic Analysis with Complex Genome Rearrangement Events
    Jijun Tang; Fiscal Year: 2009
    ..these problems by: (1) mathematical modeling and theoretical analysis of complex evolutionary events such as gene duplication and loss;(2) algorithm design and implementation for phylogenetics and gene order reconstruction (3) ..
  19. Cardiogenesis: Molecular Mechanisms
    Deepak Srivastava; Fiscal Year: 2013
    ..miR-1 and miR-133 are encoded in two loci as a result of a gene duplication, with identical mature sequences of miR-1-1 and miR-1-2, as well as miR-133a and miR- 133b...
  20. Structure-Function Analysis of Leishmania MIT
    Andreas Seyfang; Fiscal Year: 2006
    ..superfamily of membrane transporters with 12 transmembrane domains that are thought to have evolved through gene duplication of an ancestral 6-transmembranedomain transporter...
  21. THE CONVERSION OF NONCODING SEQUENCES INTO PROTEINS
    Joanna Masel; Fiscal Year: 2013
    ..Classic models hold that mutational processes generate new phenotypes through gene duplication, domain shuffling, and other mechanisms that modify existing genes rather than making new ones...
  22. EVOLUTION OF THE RIBONUCLEASE SUPERFAMILY
    Steven Benner; Fiscal Year: 2001
    ..will show how new biomolecular function is created in higher organisms, by mutation, insertion, deletion gene duplication and recruitment of duplicate genes...
  23. Proteomic methodologies for polyketide biosynthesis (RMI)
    MICHAEL BURKART; Fiscal Year: 2007
    ..to characterize genetically due to the fact that the large nuclear genomes of dinoflagellates contain high gene duplication with multiple intron content...
  24. Acetylcholinesterase: A Comparative Biochemical Approach
    Leo Pezzementi; Fiscal Year: 2005
    ..As a result of a gene duplication early in vertebrate evolution, humans and other vertebrates have another cholinesterase, ..
  25. CELL RECEPTORS IN COAGULATION AND ATHEROGENESIS
    SALVATORE PIZZO; Fiscal Year: 2001
    ..During the course of evolution, gene duplication and divergence occurred so that a family of complement proteins which are alpha2M homologues (C3, C4 and C5) ..
  26. REGULATION OF ALPHA-FETOPROTEIN GENE EXPRESSION
    Shirley Tilghman; Fiscal Year: 1993
    ..These serum proteins arose in evolution as the consequence of a gene duplication and are tightly linked in tandem on chromosome 5 in mice...
  27. Evolution of Chromosome-specific Low Copy Repeats
    Tamim Shaikh; Fiscal Year: 2005
    Large scale duplication of genetic material is a major force driving the evolution of genetic diversity. Gene duplication and subsequent divergence have been instrumental in the creation of new genes with specialized functional roles, a ..
  28. MODELS OF ATHEROSCLEROSIS BY TARGETED GENE DUPLICATION
    MYRON HINSDALE; Fiscal Year: 1999
    ..Her laboratory is located on the same floor as Dr. Smithies in the Department of Pathology. Trainees, students, and technicians from both laboratories share laboratory meetings and can readily exchange ideas and experimental experience. ..
  29. Fate and consequences of gene duplication in eukaryotes
    Michael Zanis; Fiscal Year: 2004
    ..from these studies will provide important information regarding the changes in gene structure following gene duplication. Given the prevalence of duplicate genes among eukaryotic genomes, the information garnered from this study ..
  30. GENETICS AND BIOCHEMISTRY OF A MURINE RETROPOSON
    Sandra Martin; Fiscal Year: 2009
    ..repetitive DNA, provides a substrate for homologous recombination of mispaired sequences, leading to gene duplication, deletion, chromosome translocation and, potentially, exon shuffling...
  31. STRUCTURE & REGULATION OF HUMAN PLATELET THROMBOSPONDIN
    Vishva Dixit; Fiscal Year: 1991
    ..code for seperate functional domains? b) Did the TSP gene evolve to its present form by mechanisms such as gene duplication and exon shuffling? 3) Investigate the mechanism by which platelet derived growth factor (PDGF) increases TSP ..
  32. Gene Duplication and Genome Evolution
    Austin Hughes; Fiscal Year: 2004
    ..in complete genome sequences will involve understanding the mechanisms by which genomes evolve, including gene duplication and deletion, duplication of genomic segments or entire genomes, and horizontal transfer of genes from one ..
  33. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin L Hughes; Fiscal Year: 2010
    ..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
  34. A global evolutionary analysis of eukaryotic duplication processes
    Xiang Gao; Fiscal Year: 2009
    DESCRIPTION (provided by applicant): Gene duplication is considered as the primary source of creating novel materials for genome evolution. It is also associated with many diseases of human genetic disorders...
  35. Nuclear integrations of mitochondrial DNA in great apes
    Nicola Anthony; Fiscal Year: 2007
    ..sequences and mtDNA break sites for identification, and to determine whether there has been subsequent gene duplication in the nucleus, addressing three questions: (a) Are the sites of integration random, or are they sequence-..
  36. Mobile Elements in Mammalian Genomes
    Sandra Martin; Fiscal Year: 2009
    ..regulatory networks, or provide a substrate for homologous recombination of mispaired sequences, leading to gene duplication, deletion, exon shuffling and chromosome translocation...
  37. GENOME EVOLUTION--POPULATION GENETIC ASPECTS
    J Walsh; Fiscal Year: 1990
    ..and is of considerable importance in developing theoretical models of evolution of new gene function via gene duplication. Theoretical models often suggest areas for future empirical work which are not obvious...
  38. GENETIC CONTROL OF COMPLEMENT C4 AND LINKAGE TO HLA
    GEOFFREY O NEILL; Fiscal Year: 1980
    ..Rga will be used to evaluate if the HLA-linked genes controlling C4, Cha and Rga have arisen as a result of gene duplication or if some other genetic mechanism is responsible for the expression of these red cell antigens...
  39. Pharmacogenetics of human cytochromes P450
    Leif Bertilsson; Fiscal Year: 2004
    ..g. gene duplication or multiduplication, or serious adverse effects in case of decreased metabolism due to defective alleles...
  40. Molecular and Structural Basis for T Cell Costimulation
    STANLEY NATHENSON; Fiscal Year: 2007
    ..The genes for costimulatory molecules are often present as tightly linked loci formed by gene duplication events, and as a consequence the members within a given family of costimulatory molecules share common ..
  41. IMMUNOGENETIC STUDIES OF B2M REGION
    Ralph Graff; Fiscal Year: 1990
    ..B2m region and its relationship to the H-2 complex will contribute to a better understanding of the role of gene duplication, chromosomal translocation and chromosomal duplication in the evolution of the mammalian genome...
  42. Alternate Splicing and Alcohol Exposure: TransExpress Hematome 1.0
    Subha Srinivasan; Fiscal Year: 2006
    ..as a mechanism used by metazoans to create functional diversity from small number of genes parallel to gene duplication, the limitations of gene microarrays are very limiting in biomarker research...
  43. TRYPANOSOME VARIANT ANTIGEN GENES
    Kenneth Stuart; Fiscal Year: 1992
    ..These experiments are designed to elucidate the processes of VSG gene duplication and control of VSG gene expression. 2...
  44. Approaches to Multiorganismal Comparative Proteomics
    Shamil Sunyaev; Fiscal Year: 2009
    ..b>Gene duplication events will be characterized in terms of the interaction pattern, such that we will seek to design approaches ..
  45. ENZYMATIC STUDIES ON SYNTHESIS OF DNA
    HIROAKI SHIZUYA; Fiscal Year: 1980
    ..has been collected in enzymes and compounds involved in DNA metabolism, biochemical processes in the gene duplication in a semiconservative manner have not been reproduced in vitro...
  46. Genetic studies - renal failure in HIV-1 transgenic mice
    Ali Gharavi; Fiscal Year: 2004
    ..transgene has integrated in the genomic locus of a novel gene, resulting in a complex rearrangement including gene duplication. We will characterize the transgene integration site and ensuing genomic re-arrangement by comparing RNA and ..
  47. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2003
    ..stochastic model for gene family evolution with special reference to evolutionary rate- pattern change after gene duplication, and implement an efficient maximum likelihood algorithm for sequence analysis; (2) develop the framework of ..
  48. Characterization of a large protein interaction network
    Andreas Wagner; Fiscal Year: 2005
    ..of this network, and an explanation of its structure in terms of its evolution via interaction turnover and gene duplication. Aim 1 is a global characterization of the yeast protein interaction network (YPIN)...
  49. NEURAL CONTROL OF A MOTOR PROGRAM
    James Thomas; Fiscal Year: 2002
    ..We will also continue genetic screens to identify additional potential targets. ..
  50. Proteogenomic Analysis of C. elegans
    James Thomas; Fiscal Year: 2007
    ..elegans proteome and a high-throughput pipeline that will allow similar analysis of any complex animal or plant proteome whose genome sequence is available. [unreadable] [unreadable] [unreadable]..
  51. GENETIC ANALYSIS OF CHEMOSENSATION IN C ELEGANS
    James Thomas; Fiscal Year: 2003
    ..All of the pathways under study here correspond to important regulatory pathways in humans, and many of the genes are affected in various inherited disorders. ..
  52. Statistical Studies of Genomic Evolution
    Masatoshi Nei; Fiscal Year: 2009
    ..This study is expected to give important information on the molecular mechanism of gene duplication, gene death, inter chromosomal gene transfer, etc...
  53. HUMAN DNA POLYMORPHISM AND EVOLUTION
    Wen Hsiung Li; Fiscal Year: 2001
    ..The new methods and some existing methods will used to analyze the data to be obtained. The new methods will be accessible on the World Wide Web. ..
  54. Cis-regulatory motif variants and evolution of gene regulation in yeasts
    Wen Hsiung Li; Fiscal Year: 2009
    ....
  55. MOLECULAR COEVOLUTION OF GROWTH HORMONE AND ITS RECEPTOR
    Wen Hsiung Li; Fiscal Year: 2002
    ..For amino acid differences with observed significant effects on binding, determine their collective effect in combinations. 6. Conduct statistical analyses of data to characterize evolution of GH and GHR. ..
  56. Mutation Rate Variation Among Human Genomic Regions
    Wen Hsiung Li; Fiscal Year: 2004
    ..Sequence each of them in chimpanzee, gorilla, orangutan, siamang, baboon and colobus. 4. To conduct statistical analyses of the new and existing data to address the above issues. ..
  57. Evolution of vertebrate sensory genes
    Jianzhi Zhang; Fiscal Year: 2010
    ..These studies will also help understand human smell and taste variations and disorders. ..
  58. Evolution of Duplicate Genes at the Genomic Level
    Wen Hsiung Li; Fiscal Year: 2005
    ..A computer software package for the methods in (1) and (2) will be developed. 3. To assess the extents of gene duplication in various eukaryotic genomes...
  59. MARINER TRANSPOSONS OF MAMMALS
    Hugh Robertson; Fiscal Year: 2001
    ..It will also reveal how occasionally particular copies of transposons can become integral parts of their host genetic complements. ..
  60. Genome-Wide Analysis of Gene Duplication in Vertebrates
    MARIE DURAND; Fiscal Year: 2004
    ..Isolated examples of duplicated regions support this theory, but a genome-wide study of mammalian gene duplication and subsequent functional diversification has not been attempted...
  61. Experimental evolution of ligand-receptor relationships
    Joseph Thornton; Fiscal Year: 2005
    ..abstract_text> ..
  62. Elucidating the origins and functions of unknown genes
    Howard Ochman; Fiscal Year: 2009
    ..By combining experimental and bioinformatic approaches, the present proposal will analyze the origins, functions and structural properties of ORFans, and how they have assumed key roles in cellular function. ..