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THE CHARACTERIZATION of LACTATE DEHYDROGENASE GENES in RAINBOW SMELT (Osmerus Mordax)

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THE CHARACTERIZATION of LACTATE DEHYDROGENASE GENES in RAINBOW SMELT (Osmerus Mordax) THE CHARACTERIZATION OF LACTATE DEHYDROGENASE GENES IN RAINBOW SMELT (Osmerus mordax) by Xuezheng (Jenny) Ma B.Sc. (Honours), Saint Mary’s University, 2007 THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE In the Department of Molecular Biology and Biochemistry © Xuezheng (Jenny) Ma 2009 SIMON FRASER UNIVERSITY Summer 2009 All rights reserved. This work may not be reproduced in whole or in part, by photocopy or other means, without permission of the author. APPROVAL Name: Xuezheng (Jenny) Ma Degree: Master of Science Title of Thesis: The Characterization of Lactate Dehydrogenase genes in rainbow smelt (Osmerus mordax) Examining Committee: Chair: Dr. David L. Baillie Professor, Department of Molecular Biology and Biochemistry ______________________________________ Dr. William S. Davidson Senior Supervisor Professor, Department of Molecular Biology and Biochemistry ______________________________________ Dr. Jack N. Chen Supervisor Associate Professor, Department of Molecular Biology and Biochemistry ______________________________________ Dr. Christopher T. Beh Supervisor Associate Professor, Department of Molecular Biology and Biochemistry ______________________________________ Dr. Felix Breden Internal Examiner Professor, Department of Biological Sciences Date Defended/Approved: August-17-2009 ii Declaration of Partial Copyright Licence The author, whose copyright is declared on the title page of this work, has granted to Simon Fraser University the right to lend this thesis, project or extended essay to users of the Simon Fraser University Library, and to make partial or single copies only for such users or in response to a request from the library of any other university, or other educational institution, on its own behalf or for one of its users. The author has further granted permission to Simon Fraser University to keep or make a digital copy for use in its circulating collection (currently available to the public at the “Institutional Repository” link of the SFU Library website <www.lib.sfu.ca> at: <http://ir.lib.sfu.ca/handle/1892/112>) and, without changing the content, to translate the thesis/project or extended essays, if technically possible, to any medium or format for the purpose of preservation of the digital work. The author has further agreed that permission for multiple copying of this work for scholarly purposes may be granted by either the author or the Dean of Graduate Studies. It is understood that copying or publication of this work for financial gain shall not be allowed without the author’s written permission. Permission for public performance, or limited permission for private scholarly use, of any multimedia materials forming part of this work, may have been granted by the author. This information may be found on the separately catalogued multimedia material and in the signed Partial Copyright Licence. While licensing SFU to permit the above uses, the author retains copyright in the thesis, project or extended essays, including the right to change the work for subsequent purposes, including editing and publishing the work in whole or in part, and licensing other parties, as the author may desire. The original Partial Copyright Licence attesting to these terms, and signed by this author, may be found in the original bound copy of this work, retained in the Simon Fraser University Archive. Simon Fraser University Library Burnaby, BC, Canada Last revision: Spring 09 ABSTRACT Lactate Dehydrogenase isozymes (LDH-A, LDH-B and LDH-C) represent the classical example of a multi-gene system derived by successive gene duplications. By investigating the genes encoding the LDH isozymes in rainbow smelt, a diploid out-group of the tetraploid salmonids, I sought to gain insight into the effect of a whole genome duplication superimposed upon more ancient gene duplications. I isolated rainbow smelt BAC clones containing the LDH-A, LDH-B and LDH-C genes, made shotgun libraries of three representative BACs and annotated the sequences. I characterized the smelt LDH genes with respect to structure, tissue expression and genome organization. This information was used for comparative genomic analyses with the LDH genes from Atlantic salmon. There was no evidence for positive selection, an expectation of neo- functionalization, but different rates of amino acid substitutions between and within lineages were evident in the LDH-A and LDH-B salmonid duplicates. LDH- B1 and LDH-B2 in salmonids have experienced sub-functionalization. Keywords: Gene duplication; Genome duplication; Lactate dehydrogenase; Rainbow smelt; Salmonids iii DEDICATION To my parents: Lixin Ma and Chunrong Wang, grandparents: Shaoquan Wang and Shuqin Zhang. iv ACKNOWLEDGEMENTS I would sincerely like to thank my senior supervisor Dr. William Davidson, for giving me the opportunity to work on this project, and for his patience, encouragement, understanding help and financial support. I also would like to extend my thanks to all past and present members in Davidson Lab, for their help and support during my Master project. Finally, I would like to bring my special thanks to my grandparents and parents, for their never-ending love and support. v TABLE OF CONTENTS Approval .............................................................................................................. ii Abstract .............................................................................................................. iii Dedication .......................................................................................................... iv Acknowledgements ............................................................................................ v Table of Contents .............................................................................................. vi List of Figures .................................................................................................... ix List of Tables .................................................................................................... xii Chapter 1: Introduction ...................................................................................... 1 1.1 Gene duplication ......................................................................................... 1 1.1.1 Early gene duplication research ............................................................ 2 1.2 Mechanisms of gene duplication ................................................................. 2 1.2.1 Tandem duplication ............................................................................... 3 1.2.2 Drawbacks of gene duplication ............................................................. 5 1.2.3 Retrotransposition ................................................................................. 5 1.2.4 Polyploidy.............................................................................................. 6 1.2.5 Shortcomings of polyploidy ................................................................... 8 1.3 The consequences of gene duplication ....................................................... 9 1.3.1 Nonfunctionalization ............................................................................ 11 1.3.2 Neofunctionalization ............................................................................ 12 1.3.3 Subfunctionalization ............................................................................ 13 1.4 Evidence for genome duplication in vertebrates (2R/3R/4R) ..................... 14 1.5 Evolution of fish ......................................................................................... 17 1.5.1 Fish species evolution ......................................................................... 17 1.5.2 Teleost gene and genome duplication ................................................ 20 1.5.3 Salmonidae and Osmeridae ................................................................ 21 1.6 Isozymes and gene duplication ................................................................. 25 1.6.1 Molecular basis of isozymes ............................................................... 25 1.6.2 LDH function ....................................................................................... 26 1.6.3 LDH gene control ................................................................................ 28 1.6.4 Kinetics and tissue specificity of LDH ................................................. 29 1.6.5 Evolution of LDH ................................................................................. 31 1.7 LDH gene duplication in Salmonids ........................................................... 39 1.7.1 LDH in salmonids ................................................................................ 39 1.7.2 LDH in rainbow smelt .......................................................................... 42 1.7.3 Genomic resources for rainbow smelt ................................................. 42 vi 1.8 Purpose of thesis ....................................................................................... 43 Chapter 2: Materials and methods .................................................................. 44 2.1 Rainbow smelt LDH probes and design of gene specific primers design ............................................................................................... 44 2.1.1 PCR protocol ....................................................................................... 44 2.1.2 LDH-A ................................................................................................
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