Wong, Man Chun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 141-146). / Abstracts in English and Chinese. / Abstract --- p.iii / 摘要 --- p.v / Acknowledgments --- p.vii / Table of contents --- p.viii / List of tables --- p.xi / List of figures --- p.xii / List of appendix --- p.xv / Abbreviations --- p.xvi / Chapter Chapter 1 --- Literature review --- p.1 / Chapter 1.1 --- Background of Lentinula edodes --- p.1 / Chapter 1.2 --- Life cycle and mating system of Lentinula edodes --- p.1 / Chapter 1.3 --- Breeding and strain improvement --- p.5 / Chapter 1.4 --- Application of molecular markers --- p.6 / Chapter 1.5 --- Objectives and long term significance --- p.9 / Chapter Chapter 2 --- Genome survey sequencing and preliminary analysis --- p.11 / Chapter 2.1 --- Introduction --- p.11 / Chapter 2.1.1 --- Genome sequencing of basidiomycetes --- p.11 / Chapter 2.1.2 --- Polymerase chain reaction-single strand conformational polymorphism --- p.12 / Chapter 2.1.3 --- Sequencing chemistry --- p.13 / Chapter 2.2 --- Materials and methods --- p.15 / Chapter 2.2.1 --- Strain and DNA extraction --- p.15 / Chapter 2.2.2 --- PCR-SSCP analysis --- p.15 / Chapter 2.2.3 --- Shotgun sequencing and sequence assembly --- p.17 / Chapter 2.2.4 --- Comparison with 5 basidiomycetes --- p.17 / Chapter 2.3 --- Results --- p.19 / Chapter 2.3.1 --- PCR-SSCP --- p.19 / Chapter 2.3.2 --- Shotgun sequencing and assembly --- p.21 / Chapter 2.3.3 --- Comparison with 5 basidiomycetes --- p.22 / Chapter 2.4 --- Discussion --- p.30 / Chapter Chapter 3 --- Cloning of A mating-type locus of Lentinula edodes --- p.33 / Chapter 3.1 --- Introduction --- p.33 / Chapter 3.2 --- Materials and methods --- p.35 / Chapter 3.2.1 --- Genome sequencing and assembly --- p.35 / Chapter 3.2.2 --- Genomic screening of A-mating type genes --- p.35 / Chapter 3.2.3 --- Gap filling and sequence confirmation --- p.36 / Chapter 3.2.4 --- Alignment of overlapping sequences to give contiguous sequence --- p.37 / Chapter 3.2.5 --- Open reading frame prediction and protein homolog search --- p.37 / Chapter 3.2.6 --- Conserved domain search --- p.37 / Chapter 3.2.7 --- Testing for polymorphism --- p.38 / Chapter 3.3 --- Results --- p.39 / Chapter 3.3.1 --- Genomic screening of A-mating type genes --- p.39 / Chapter 3.3.2 --- Gap filling and sequence confirmation --- p.45 / Chapter 3.3.3 --- Protein homologs and putative protein domains --- p.48 / Chapter 3.3.4 --- Polymorphism of A mating-type genes --- p.53 / Chapter 3.4 --- Discussion --- p.55 / Chapter 3.4.1 --- Genome mining of the A mating-type locus of L. edodes --- p.55 / Chapter 3.4.2 --- Genomic structure of the A mating-type region in L. edodes --- p.55 / Chapter 3.4.3 --- Functional protein domains in A mating-type genes --- p.56 / Chapter 3.4.4 --- Polymorphism of A mating- type locus --- p.58 / Chapter 3.4.5 --- Conclusion and future perspectives --- p.59 / Chapter Chapter 4 --- Simple sequence repeat (SSR) markers development --- p.60 / Chapter 4.1 --- Introduction --- p.60 / Chapter 4.2 --- Materials and methods --- p.62 / Chapter 4.2.1 --- Strains --- p.62 / Chapter 4.2.2 --- Datasets for SSRs mining --- p.63 / Chapter 4.2.3 --- in silico detection of SSR motifs and primer design --- p.63 / Chapter 4.2.4 --- SSR amplification --- p.64 / Chapter 4.2.5 --- Cloning and sequencing of PCR products --- p.64 / Chapter 4.2.6 --- Testing for polymorphism --- p.65 / Chapter 4.3 --- Results --- p.66 / Chapter 4.3.1 --- in silico detection of SSR motifs and primer design --- p.66 / Chapter 4.3.2 --- SSR amplification --- p.69 / Chapter 4.3.3 --- SSR polymorphism --- p.83 / Chapter 4.4 --- Discussion --- p.86 / Chapter 4.4.1 --- Efficiency of in silico detection of SSR motifs and primer design --- p.86 / Chapter 4.4.2 --- Effectiveness and polymorphism of SSR primer pairs --- p.89 / Chapter 4.4.3 --- Conclusion and future perspectives --- p.90 / Chapter Chapter 5 --- High-throughput sequencing of AP-PCR amplicons for SCAR markers development and phylogenetic analysis --- p.91 / Chapter 5.1 --- Introduction --- p.91 / Chapter 5.2 --- Materials and methods --- p.94 / Chapter 5.2.1 --- Strains --- p.94 / Chapter 5.2.2 --- AP-PCR analysis --- p.94 / Chapter 5.2.3 --- Re-amplification of AP-PCR amplicons --- p.96 / Chapter 5.2.4 --- GS-FLX sequencing --- p.96 / Chapter 5.2.5 --- Strain-specific sequences identification --- p.97 / Chapter 5.2.6 --- SCAR marker analysis --- p.97 / Chapter 5.2.7 --- Phylogenetic analysis --- p.99 / Chapter 5.3 --- Results --- p.100 / Chapter 5.3.1 --- AP-PCR analysis --- p.100 / Chapter 5.3.2 --- Re-amplification of AP-PCR amplicons --- p.100 / Chapter 5.3.3 --- GS-FLX sequencing and strain-specific sequence identification --- p.103 / Chapter 5.3.4 --- SCAR marker analysis --- p.106 / Chapter 5.3.5 --- Phylogenetic analysis --- p.108 / Chapter 5.4 --- Discussion --- p.111 / Chapter 5.4.1 --- Sensitivity of band detection --- p.111 / Chapter 5.4.2 --- SCAR marker development --- p.111 / Chapter 5.4.3 --- Phylogenetic analysis --- p.113 / Chapter 5.4.4 --- Conclusion --- p.114 / Chapter Chapter 6 --- Concluding remarks --- p.115 / Chapter 6.1 --- Project summary --- p.115 / Chapter 6.2 --- Future perspectives --- p.119 / Appendix --- p.121 / References --- p.141
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_326765 |
| Date | January 2009 |
| Contributors | Wong, Man Chun., Chinese University of Hong Kong Graduate School. Division of Life Sciences. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | print, xvi, 146 leaves : ill. (some col.) ; 30 cm. |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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