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. doi 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
  2. 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
  3. 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
  4. doi 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
  5. 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
  6. 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
  7. doi Synteny and collinearity in plant genomes
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Science 320:486-8. 2008
  8. 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
  9. 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
  10. 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

Research Grants

Detail Information

Publications266 found, 100 shown here

  1. doi 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...
  2. 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...
  3. 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...
  4. doi 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...
  5. 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 ..
  6. 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...
  7. doi 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...
  8. 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...
  9. 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 ..
  10. 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...
  11. 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
    ....
  12. doi 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. doi 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...
  14. 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
    ....
  15. doi 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...
  16. doi 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 ..
  17. 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
    ....
  18. 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...
  19. 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...
  20. 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.
  21. 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...
  22. doi 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. doi 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...
  29. 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...
  30. 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...
  31. 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 ..
  32. 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.
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. doi 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...
  39. 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...
  40. 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
    ....
  41. 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...
  42. 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...
  43. doi 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...
  44. 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...
  45. 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...
  46. 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...
  47. doi 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...
  48. doi 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...
  49. 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...
  50. doi 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...
  51. 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
    ....
  52. 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...
  53. 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 ..
  54. 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
    ....
  55. doi 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...
  56. 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...
  57. 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...
  58. 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
    ....
  59. 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...
  60. doi 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...
  61. doi 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...
  62. 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...
  63. doi 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.
  64. 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...
  65. 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...
  66. 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
    ....
  67. 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...
  68. 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...
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. doi 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 ..
  74. 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...
  75. 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...
  76. ncbi Duplication of the entire 22.9 Mb human chromosome 21 syntenic region on mouse chromosome 16 causes cardiovascular and gastrointestinal abnormalities
    Zhongyou Li
    Department of Cancer Genetics and Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
    Hum Mol Genet 16:1359-66. 2007
    ..This new mouse model represents a powerful tool to further understand the molecular and cellular mechanisms of Down syndrome...
  77. pmc Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
    Orjan Akerborg
    School for Computer Science and Communication, Royal Institute of Technology, SE 10044 Stockholm, Sweden
    Proc Natl Acad Sci U S A 106:5714-9. 2009
    We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families...
  78. 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...
  79. 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.
  80. pmc Complexity, connectivity, and duplicability as barriers to lateral gene transfer
    Alon Wellner
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel, 69978
    Genome Biol 8:R156. 2007
    ....
  81. pmc The resolution of sexual antagonism by gene duplication
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 2703, USA
    Genetics 187:919-37. 2011
    ..Recent verbal models suggest that gene duplication and sex-specific cooption of paralogs might resolve sexual antagonism and facilitate evolutionary divergence ..
  82. doi Comparison of pig, sheep and chicken SCD5 homologs: Evidence for an early gene duplication event
    Andrea J Lengi
    Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Comp Biochem Physiol B Biochem Mol Biol 150:440-6. 2008
    ..This is the first report of an SCD5 homolog in a non-mammalian species, and suggests that SCD5 may be the result of an early gene duplication event that occurred before the divergence of mammals.
  83. pmc Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Biol 8:R50. 2007
    b>Gene duplication provides raw material for the generation of new functions, but most duplicates are rapidly lost due to the initial redundancy in gene function. How gene function diversifies following duplication is largely unclear...
  84. pmc Trichomonas transmembrane cyclases result from massive gene duplication and concomitant development of pseudogenes
    Jike Cui
    Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, USA
    PLoS Negl Trop Dis 4:e782. 2010
    ..With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here a family of approximately 123 Trichomonas genes that encode transmembrane adenylyl cyclases (TMACs)...
  85. pmc Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts
    Erin S Kelleher
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 3:e148. 2007
    ..Additionally, pervasive gene duplication, adaptive evolution, and rapid acquisition of a novel digestive function by the female reproductive tract ..
  86. ncbi Characterization, polymorphism, and evolution of MHC class II B genes in birds of prey
    Miguel Alcaide
    Estacion Biologica de Donana, CSIC Pabellón de Perú, Avda Ma Luisa s n, 41013, Sevilla, Spain
    J Mol Evol 65:541-54. 2007
    ..Finally, through interlocus comparisons and phylogenetic analysis, we also discuss genetic evidence for concerted and transspecies evolution in the raptor MHC...
  87. pmc OPTIC: orthologous and paralogous transcripts in clades
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK
    Nucleic Acids Res 36:D267-70. 2008
    ..Gene predictions, multiple alignments and phylogenetic trees are freely available to browse and download from http://genserv.anat.ox.ac.uk/clades. Further genomes and clades will be added in the future...
  88. doi The avian Toll-Like receptor pathway--subtle differences amidst general conformity
    Paul Cormican
    School of Biochemistry and Immunology, Trinity College, University of Dublin, Dublin 2, Ireland
    Dev Comp Immunol 33:967-73. 2009
    ..The TLR receptors show a pattern of gene duplication and gene loss in both avian species when compared to mammals...
  89. pmc Relaxation of yeast mitochondrial functions after whole-genome duplication
    Huifeng Jiang
    Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
    Genome Res 18:1466-71. 2008
    ..This new energy production strategy could have led to the relaxation of mitochondrial function in the relevant yeast species...
  90. pmc Protease gene duplication and proteolytic activity in Drosophila female reproductive tracts
    Erin S Kelleher
    Department of Ecology and Evolutionary Biology, University of Arizona, USA
    Mol Biol Evol 26:2125-34. 2009
    ..tract proteins in the cactophilic fruit fly Drosophila arizonae, identified pervasive, lineage-specific gene duplication amongst secreted proteases...
  91. pmc Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years
    Andrew R Carson
    The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
    BMC Evol Biol 9:156. 2009
    ..To eliminate genes that have been conserved due to strong purifying selection, our analysis also required at least one intron to have retained high sequence similarity between paralogues...
  92. pmc Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice
    Thomas Thiel
    IPK Gatersleben, Corrensstr, 3, 06466 Gatersleben, Germany
    BMC Evol Biol 9:209. 2009
    ....
  93. pmc Transcript profiling provides evidence of functional divergence and expression networks among ribosomal protein gene paralogs in Brassica napus
    Carrie A Whittle
    Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Canada S7N 0W9
    Plant Cell 21:2203-19. 2009
    ....
  94. pmc InParanoid 6: eukaryotic ortholog clusters with inparalogs
    Ann Charlotte Berglund
    Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala, Sweden
    Nucleic Acids Res 36:D263-6. 2008
    ..A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters...
  95. doi Metabolic adaptation after whole genome duplication
    Milan J A van Hoek
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    Mol Biol Evol 26:2441-53. 2009
    ..This explains why WGD, while pivotal in the evolution of many lineages and an apparent "easy" genetic operator, occurs relatively rarely...
  96. pmc Rapid diversification of cell signaling phenotypes by modular domain recombination
    Sergio G Peisajovich
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
    Science 328:368-72. 2010
    ..Thus, novel linkages between preexisting domains may have a major role in the evolution of protein networks and novel phenotypic behaviors...
  97. pmc Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression
    Stephanie Bertrand
    Molecular Zoology, Institut de Génomique Fonctionelle de Lyon UMR 5242 du CNRS, INRA, IFR128 Biosciences Lyon Gerland, Universite de Lyon, UCB Ecole Normale Supérieure de Lyon, France
    PLoS Genet 3:e188. 2007
    ..Altogether, this expression database of NRs provides novel routes for leading investigation into the biological function of each individual NR as well as for the study of their combinatorial regulatory circuitry within the superfamily...
  98. pmc Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication
    Jeong Hwan Mun
    Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin ro, Gwonseon gu, Suwon 441 707, Korea
    Genome Biol 10:R111. 2009
    ..rapa, which is a strong challenge of structural and comparative crop genomics...
  99. pmc Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies
    Adriana D Briscoe
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 107:3628-33. 2010
    ..Functional diversification of the UV-sensitive visual pigments may help explain why the yellow wing pigments of Heliconius are so colorful in the UV range compared to the yellow pigments of close relatives lacking the UV opsin duplicate...

Research Grants85

  1. 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...
  2. ISLET CELL MEMBRANE ANTIBODIES IN DIABETES
    Ake Lernmark; Fiscal Year: 1992
    ..isoforms important in several autoimmune diseases, including Stiff-Man syndrome, may be explained in part by gene duplication. We confirm the mapping of GAD1 (3...
  3. Molecular genetics of Pelizaeus-Merzbacher disease
    Grace Hobson; Fiscal Year: 2009
    ..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...
  4. Molecular genetics of Pelizaeus-Merzbacher disease
    Grace M Hobson; Fiscal Year: 2010
    ..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...
  5. Functional genomic approaches to duplicate gene evolution
    Jianzhi Zhang; Fiscal Year: 2010
    ..b>Gene duplication is wildly regarded as the primary source of new genes, but the general patterns and mechanisms of functional ..
  6. Functional genomic approaches to duplicate gene evolution
    Jianzhi Zhang; Fiscal Year: 2010
    ..b>Gene duplication is wildly regarded as the primary source of new genes, but the general patterns and mechanisms of functional ..
  7. 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...
  8. 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...
  9. 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...
  10. 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, ..
  11. CELL RECEPTORS IN COAGULATION AND ATHEROGENESIS
    SALVATORE PIZZO; Fiscal Year: 1992
    ..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) ..
  12. EXPRESSION AND FUNCTION OF CONE PIGMENT GENES
    Jay Neitz; Fiscal Year: 2006
    ..The M and L genes lie in a head-to-tail tandem array on the X-chromosome and were produced by a gene duplication event that is estimated to have occurred in the primate lineage about 35-60 million years ago...
  13. GENE CONVERSION IN MICE
    John Schimenti; Fiscal Year: 1999
    ..The era of molecular biology has dramatically illustrated the role of gene duplication in genome evolution...
  14. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin Hughes; Fiscal Year: 2002
    ..immune system evolve more rapidly than those expressed in other tissues; and (6) to understand the roles of gene duplication, interlocus recombination, and natural selection in the diversification of immune system gene families (..
  15. GENETICS AND BIOCHEMISTRY OF A MURINE RETROPOSON
    Sandra Martin; Fiscal Year: 2001
    ..repetitive DNA, provides a substrate for homologous recombination of mispaired sequences, leading to gene duplication, deletion, chromosome translocation and, potentially, exon shuffling...
  16. COMPARATIVE MOLECULAR SEQUENCE ANALYSIS
    Sudhir Kumar; Fiscal Year: 2009
    ..species, and gene families; [ii] estimate the confidence intervals for times of species divergence and gene duplication events; [iii] deduce tracks of adaptive evolution in proteins, genes, and codons; [iv] test alternative ..
  17. COMPARATIVE MOLECULAR SEQUENCE ANALYSIS
    Sudhir Kumar; Fiscal Year: 2007
    ..species, and gene families; [ii] estimate the confidence intervals for times of species divergence and gene duplication events; [iii] deduce tracks of adaptive evolution in proteins, genes, and codons; [iv] test alternative ..
  18. Genetics & Biochemistry of a Murine Retroposon
    Sandra Martin; Fiscal Year: 2005
    ..repetitive DNA, provides a substrate for homologous recombination of mispaired sequences, leading to gene duplication, deletion, chromosome translocation and, potentially, exon shuffling...
  19. IRBP--STRUCTURE/FUNCTION
    Federico Gonzalez Fernandez; Fiscal Year: 2002
    ..It is reasoned that through gene duplication the structure of the modules diverged, creating sites tailored for each of IRBP's physiological ligands...
  20. 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)...
  21. 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) ..
  22. POPULATION GENETICS OF MOBILE ELEMENTS
    Lynn Jorde; Fiscal Year: 2007
    ..Our understanding of genetic disease will also be enhanced by a better understanding of the role of these elements in DNA repair and in gene duplication and deletion.
  23. 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 ..