Literature DB >> 19796838

The origins and impact of primate segmental duplications.

Tomas Marques-Bonet1, Santhosh Girirajan, Evan E Eichler.   

Abstract

Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses.

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Year:  2009        PMID: 19796838      PMCID: PMC2847396          DOI: 10.1016/j.tig.2009.08.002

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  88 in total

1.  SMN gene duplication and the emergence of the SMN2 gene occurred in distinct hominids: SMN2 is unique to Homo sapiens.

Authors:  C F Rochette; N Gilbert; L R Simard
Journal:  Hum Genet       Date:  2001-03       Impact factor: 4.132

2.  Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17.

Authors:  Hildegard Kehrer-Sawatzki; Bettina Schreiner; Simone Tänzer; Matthias Platzer; Stefan Müller; Horst Hameister
Journal:  Am J Hum Genet       Date:  2002-07-01       Impact factor: 11.025

3.  A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon.

Authors:  Klaus Fellermann; Daniel E Stange; Elke Schaeffeler; Hartmut Schmalzl; Jan Wehkamp; Charles L Bevins; Walter Reinisch; Alexander Teml; Matthias Schwab; Peter Lichter; Bernhard Radlwimmer; Eduard F Stange
Journal:  Am J Hum Genet       Date:  2006-07-12       Impact factor: 11.025

4.  The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs.

Authors:  L T Reiter; T Murakami; T Koeuth; R A Gibbs; J R Lupski
Journal:  Hum Mol Genet       Date:  1997-09       Impact factor: 6.150

5.  Trichromatic colour vision in New World monkeys.

Authors:  G H Jacobs; M Neitz; J F Deegan; J Neitz
Journal:  Nature       Date:  1996-07-11       Impact factor: 49.962

6.  Shotgun sequence assembly and recent segmental duplications within the human genome.

Authors:  Xinwei She; Zhaoshi Jiang; Royden A Clark; Ge Liu; Ze Cheng; Eray Tuzun; Deanna M Church; Granger Sutton; Aaron L Halpern; Evan E Eichler
Journal:  Nature       Date:  2004-10-21       Impact factor: 49.962

7.  Defensins and the convergent evolution of platypus and reptile venom genes.

Authors:  Camilla M Whittington; Anthony T Papenfuss; Paramjit Bansal; Allan M Torres; Emily S W Wong; Janine E Deakin; Tina Graves; Amber Alsop; Kyriena Schatzkamer; Colin Kremitzki; Chris P Ponting; Peter Temple-Smith; Wesley C Warren; Philip W Kuchel; Katherine Belov
Journal:  Genome Res       Date:  2008-05-07       Impact factor: 9.043

8.  Death and resurrection of the human IRGM gene.

Authors:  Cemalettin Bekpen; Tomas Marques-Bonet; Can Alkan; Francesca Antonacci; Maria Bruna Leogrande; Mario Ventura; Jeffrey M Kidd; Priscillia Siswara; Jonathan C Howard; Evan E Eichler
Journal:  PLoS Genet       Date:  2009-03-06       Impact factor: 5.917

9.  RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.

Authors:  Vladimir V Kapitonov; Jerzy Jurka
Journal:  PLoS Biol       Date:  2005-05-24       Impact factor: 8.029

10.  Population bottlenecks as a potential major shaping force of human genome architecture.

Authors:  Adrian Gherman; Peter E Chen; Tanya M Teslovich; Pawel Stankiewicz; Marjorie Withers; Carl S Kashuk; Aravinda Chakravarti; James R Lupski; David J Cutler; Nicholas Katsanis
Journal:  PLoS Genet       Date:  2007-07       Impact factor: 5.917

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  72 in total

Review 1.  Origins, evolution, and phenotypic impact of new genes.

Authors:  Henrik Kaessmann
Journal:  Genome Res       Date:  2010-07-22       Impact factor: 9.043

2.  Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.

Authors:  Aaron R Quinlan; Royden A Clark; Svetlana Sokolova; Mitchell L Leibowitz; Yujun Zhang; Matthew E Hurles; Joshua C Mell; Ira M Hall
Journal:  Genome Res       Date:  2010-03-22       Impact factor: 9.043

3.  Copy number variation of individual cattle genomes using next-generation sequencing.

Authors:  Derek M Bickhart; Yali Hou; Steven G Schroeder; Can Alkan; Maria Francesca Cardone; Lakshmi K Matukumalli; Jiuzhou Song; Robert D Schnabel; Mario Ventura; Jeremy F Taylor; Jose Fernando Garcia; Curtis P Van Tassell; Tad S Sonstegard; Evan E Eichler; George E Liu
Journal:  Genome Res       Date:  2012-02-02       Impact factor: 9.043

4.  Evolutionary biology: The handiwork of tinkering.

Authors:  Paul Flicek
Journal:  Nature       Date:  2013-08-08       Impact factor: 49.962

5.  Genome reference and sequence variation in the large repetitive central exon of human MUC5AC.

Authors:  Xueliang Guo; Shuo Zheng; Hong Dang; Rhonda G Pace; Jaclyn R Stonebraker; Corbin D Jones; Frank Boellmann; George Yuan; Prashamsha Haridass; Olivier Fedrigo; David L Corcoran; Max A Seibold; Swati S Ranade; Michael R Knowles; Wanda K O'Neal; Judith A Voynow
Journal:  Am J Respir Cell Mol Biol       Date:  2014-01       Impact factor: 6.914

Review 6.  In transition: primate genomics at a time of rapid change.

Authors:  Jeffrey Rogers
Journal:  ILAR J       Date:  2013

7.  Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events.

Authors:  Amir Ali Abbasi
Journal:  Nat Rev Genet       Date:  2010-01-06       Impact factor: 53.242

8.  Genes Relocated Between Drosophila Chromosome Arms Evolve Under Relaxed Selective Constraints Relative to Non-Relocated Genes.

Authors:  Margaret L I Hart; Ban L Vu; Quinten Bolden; Keith T Chen; Casey L Oakes; Lejla Zoronjic; Richard P Meisel
Journal:  J Mol Evol       Date:  2018-06-21       Impact factor: 2.395

9.  Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants.

Authors:  Xiaofan Zhou; Zhenguo Lin; Hong Ma
Journal:  Genome Biol       Date:  2010-04-06       Impact factor: 13.583

10.  A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay.

Authors:  Santhosh Girirajan; Jill A Rosenfeld; Gregory M Cooper; Francesca Antonacci; Priscillia Siswara; Andy Itsara; Laura Vives; Tom Walsh; Shane E McCarthy; Carl Baker; Heather C Mefford; Jeffrey M Kidd; Sharon R Browning; Brian L Browning; Diane E Dickel; Deborah L Levy; Blake C Ballif; Kathryn Platky; Darren M Farber; Gordon C Gowans; Jessica J Wetherbee; Alexander Asamoah; David D Weaver; Paul R Mark; Jennifer Dickerson; Bhuwan P Garg; Sara A Ellingwood; Rosemarie Smith; Valerie C Banks; Wendy Smith; Marie T McDonald; Joe J Hoo; Beatrice N French; Cindy Hudson; John P Johnson; Jillian R Ozmore; John B Moeschler; Urvashi Surti; Luis F Escobar; Dima El-Khechen; Jerome L Gorski; Jennifer Kussmann; Bonnie Salbert; Yves Lacassie; Alisha Biser; Donna M McDonald-McGinn; Elaine H Zackai; Matthew A Deardorff; Tamim H Shaikh; Eric Haan; Kathryn L Friend; Marco Fichera; Corrado Romano; Jozef Gécz; Lynn E DeLisi; Jonathan Sebat; Mary-Claire King; Lisa G Shaffer; Evan E Eichler
Journal:  Nat Genet       Date:  2010-02-14       Impact factor: 38.330

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