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Comparative Genome Analysis Between the Atlantic Salmon Sex Chromosome and the Genomes of Other Teleosts

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Comparative Genome Analysis Between the Atlantic Salmon Sex Chromosome and the Genomes of Other Teleosts COMPARATIVE GENOME ANALYSIS BETWEEN THE ATLANTIC SALMON SEX CHROMOSOME AND THE GENOMES OF OTHER TELEOSTS by Teng-Kai (Kevin) Huang B. Sc., Simon Fraser University, 2006 THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE In the Department of Molecular Biology and Biochemistry © Teng-Kai (Kevin) Huang 2009 SIMON FRASER UNIVERSITY Spring 2009 All rights reserved. This work may not be reproduced jill whole or in part, by photocopy or other means, without permission of the author. APPROVAL Name: Teng-Kai (Kevin) Huang Degree: Master of Science Title of Thesis: Comparative Genome Analysis between the Atlantic Salmon Sex Chromosome and the Genomes of Other Teleosts Examining Committee: Chair: Dr. Andrew J. Bennet Professor, Department of Chemistry 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. Norbert H. Haunerland Supervisor Professor, Department of Biological Sciences Dr. Fiona S. L. Brinkman Public Examiner Associate Professor, Department of Molecular Biology and Biochemistry Date Defended!Approved: ii SIMON FRASER UNIVERSITY LIBRARY 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 Flraser 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 Revised: Fall 2007 ABSTRACT In Atlantic salmon, Linkage Group (LG) I contains the sex-determining locus, and from previous studies it was found that LG 1 corresponds to chromosome 2. I have completed a screen of the Atlantic salmon bacterial artificial chromosome (BAC) libraries for all known microsatellite markers on LG 1, and was able to integrate much of the physical and linkage maps in this genomic region. I have also constructed BAC minimum tiling pathways in many regions of chromosome 2, with the sequences of some of these regions being obtained. All the BAC-end sequences from the contigs assigned to Atlantic salmon LG 1 were subjected to BLASTx searches with the genomes of medaka, stickleback, zebrafish and Tetraodon. The orthologous genes found were used to identify the regions of these fish genomes that are syntenic to Atlantic salmon LG 1. Three sex­ determining gene candidates were also identified: ZFYVE27, Zmat4 and TSG118. iii ACKNOWLEDGEMENTS First of all, I would like to thank my senior supervisor, Dr. William S. Davidson, for his tremendous help for the past two years of my master program. My learning experience has been fun and enjoyable with him, and I really appreciate his kindness, patience, and support. I am grateful to all the guidance and advice that he provided me to carry out my research for the past two years, and his help on the completion of my thesis and my master degree. I thank Dr. Jack N. Chen and Dr. Norbert H. Haunerland, the members of my thesis committee, for contributing their time and expertise on my work, and their good-natured support. I am grateful too for the support from all the lab people for the past two years. I enjoyed the friendships and all the times that we had together. Especially, I need to express my gratitude and appreciation to Dr. Kazuhiro Fujiki, who taught me all the skills necessary for the two years of my master program, and shared all of his knowledge and advice with me regarding to my project. I would also like to thank Jieying Li for her help on some of the minimum tiling pathway constructions, and she has done the job very well. My appreciation also goes to Keith Boroevich for developing the Asalbase website with all the BLASTx results, and William Chow for developing the GRASP website with all the sequence annotation data. I must acknowledge all of my church friends, especially to Benson Hsu and Howard Liu, and my church pastors, Victor Pai and Dove Jang, who had prayed for me, encouraged me, and supported me for the past two years of my master program. I would not have been able to complete my master program without their support. Finally, I would like to thank my Grade 4 science teacher, Ms. Lucia Chen. She really inspired me to do science as my career through a project that we had worked together for a science competition 16 years ago, and it is this inspiration that drives me forward until this day. I am also grateful for the many support and encouragement that she gave me during the period of my thesis writing. Without her, my life could be completely different, and the completion of this thesis would be impossible. (Thank you, Ms. Chen.) IV TABLE OF CONTENTS Approval " ii Abstract " iii Acknowledgements " iv Table of Contents n ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••V List of Figures n................................................................................... vii List of Tables ix Chapter 1: Introduction 1 1.1 Sex-Determining Mechanisms 1 1.1.1 Environmental Mechanisms 1 1.1.2 Genetic Mechanisms 2 1.2 Sex-Determination and Sex Chromosome Evolution in Vertebrates 2 1.2.1 Mammals 3 1.2.2 Birds 5 1.2.3 Fishes 6 1.3 Sex-Determination in Teleost Fishes .- 9 1.3.1 Medaka 9 1.3.2 Poeciliid 10 1.3.3 Tilapia 12 1.3.4 Stickleback 14 1.3.5 Pufferfish 15 1.4 Sex-Determinations in Salmonids 16 1.5 Atlantic Salmon Linkage Group (LG) 1 19 1.6 Comparative Genome Analysis 21 1.6.1 Whole-Genome Duplication 21 1.6.2 Salmonid Genome Duplication 23 1.6.3 Comparing Genomes from Different Species 24 1.7 Aim of the Thesis 27 Chapter 2: Materials and Methods 28 2.1 Integration of Microsatellite and SNP Markers into Atlantic Salmon Linkage Group 1 28 2.1.1 Probe and Primer Design 28 2.1.2 BAC Library Screening 28 2.1.3 Positiveness Check by PCR 29 2.1.4 Identifying the Corresponding Contig 30 2.2 Chromosome "Walking" Along Atlantic Salmon Linkage Group 1 31 v 2.2.1 Probe and Primer Design 31 2.2.2 BAC Library Screening 31 2.2.3 Positiveness Check by PCR 31 2.2.4 Joining the Contigs 31 2.3 Sequencing the BAC Inserts 32 2.3.1 PCR Procedure 32 2.3.2 Subcloning the PCR Product 32 2.3.3 Insert Check by Colony PCR 33 2.3.4 Sequencing Reaction 34 2.4 BAC Sequencing Analysis and Gene Identification 35 2.5 Comparative Genome Analysis 36 Chapter 3: Results 37 3.1 Updating the Atlantic Salmon Linkage Group (LG) 1 Physical Map 37 3.1.1 An Overview of Atlantic Salmon LG 1 37 3.1.2 Incorporating Sex-Linked Microsatellte Markers into the Physical Map 39 3.2 Extension of Coverage of Atlantic Salmon LG 1 Physical Map .47 3.2.1 Chromosome Walking .47 3.2.2 Joining the Contigs 55 3.3 Minimum Tiling Pathways 57 3.3.1 Super-Contig 783 59 3.3.2 Super-Contig 332 67 3.3.3 Super-Contig 315 72 3.3.4 Super-Contig 2169 75 3.3.5 OMYlllliRA 79 3.4 Assembly and Annotation of BAC Sequences 83 3.4.1 Sequences Annotation 83 3.4.2 Genes Identified " 89 3.5 Comparative Genome Analysis 107 3.5.1 Medaka " 110 3.5.2 Stickleback " 114 3.5.3 Zebrafish 118 3.5.4 Tetraodon 122 3.6 A Comparison between the Comparative Genomics Data and the BAC Sequencing Data 125 3.7 Candidate Sex-Determining Genes 128 Chapter 4: Discussions and Conclusions 139 4.1 A Comparison between the Previous Work in Comparative Genomics and my Results 139 4.2 Future Work 141 References 143 VI LIST OF FIGURES Figure 3.1 Atlantic salmon Linkage Group 1. 38 Figure 3.2 CHORI-214 Atlantic salmon BAC library filter hybridized with BHMS7.029 probe 44 Figure 3.3 Hybridization positive BACs found by BHMS7.029 microsatellite probe were confirmed by PCR .45 Figure 3.4 Contig 332 as viewed from Asalbase .46 Figure 3.5 Checking the Orientation of BACs located at the end of a contig using PCR 53 Figure 3.6 PCR result of end BACs in contig 783, using both T7 and SP6 primers from S0065E16 54 Figure 3.7 Super-contig 783 63 Figure 3.8 Super-contig 332 69 Figure 3.9 Super-contig 315 73 Figure 3.10 Super-contig 2169 77 Figure 3.11 The region around the microsatellite marker OMYIIINRA.
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