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dc.description.abstractThe extensive studies on the insect obligate symbionts have demonstrated that the intracellular symbiosis resulted in the massive genome reduction, yet the evolution of facultative symbionts is less clear. The genus Spiroplasma contains a group of facultative symbionts that are associated with a variety of insects in natural environments, rendering them a good system to study the host adaptation and the genome evolution. Using comparative genomics approaches, I have identified several enzyme-coding substrate metabolism genes associated with pathogenicity and host adaptation in Spiroplasma, and showed that Spiroplasma continuously acquired foreign genetic fragments. The genome of the honeybee pathogen Spiroplasma melliferum IPMB4A contains a gene encodes for chitinase, which may contribute to its pathogenicity. It also contains abundant plectroviral sequences, which are associated with the extensive genome rearrangements. In freshwater crustaceans pathogen S. eriocheiris, its genome harbors 7% of the protein-coding genes that were acquired through horizontal gene transfer (HGT). Several of these genes are involved in substrate utilization and may be associated with the adaptation to aquatic environments. In addition, the pathogenicity of Spiroplasma toward mosquitoes is associated with the presence of a gene encoding for glycerol-3-phosphate oxidase (GlpO), which produces reactive oxygen species during the glycerol metabolism. In S. taiwanense, the glpO gene was acquired through HGT from species closely related to Mycoplasma mycoides, in which the knockout of glpO alleviated the pathogenicity. Moreover, the transcriptome analyses showed that the horizontally acquired genes, including the glpO gene and several of the substrate utilization genes, were expressed in the comparative level of those for glycolysis, suggesting their important roles in metabolism. In conclusion, this study shows that the Spiroplasma species frequently acquired functional genes and mobile genetic elements through HGT, which may counteract the genome degradation during the symbiosis.en_US
dc.description.tableofcontents摘要 i ABSTRACT ii TABLE OF CONTENTS iii LIST OF TABLE v LIST OF FIGURES vi 1 INTRODUCTION 1 1.1 THE GENOME EVOLUTION IN BACTERIAL SYMBIONTS 1 1.1.1 The genomic changes following host restriction in bacteria 1 1.1.2 Mechanisms of genome reduction 2 1.1.3 Difference between obligate and facultative insect symbionts 3 1.2 THE ECOLOGY AND EVOLUTION OF SPIROPLASMA 3 1.2.1 General features of Spiroplasma 3 1.2.2 Phylogenetic classification and host range 4 1.2.3 Spiroplasma genome evolution 6 1.3 RESEARCH PROPOSAL AND RATIONALE 7 2 Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium 10 2.1 INTRODUCTION 10 2.2 METHODS 11 2.2.1 Strain isolation and DNA preparation 11 2.2.2 Pulsed-field gel electrophoresis 12 2.2.3 Molecular phylogenetic inference 12 2.2.4 Serology test 13 2.2.5 Whole-genome shotgun sequencing 14 2.2.6 Genome assembly and annotation 14 2.2.7 Comparative analysis with other genomes 15 2.3 RESULTS AND DISCUSSION 16 2.3.1 Species identification and phylogenetic inference 16 2.3.2 Genome assembly and annotation 17 2.3.3 Comparative analysis with S. Melliferum KC3 and S. Citri 18 2.3.4 Comparative analysis with mycoplasma and phytoplasma 20 2.4 CONCLUSIONS 23 3 The fates of horizontally acquired genes in Spiroplasma atrichopogonis and Spiroplasma eriocheiris 33 3.1 INTRODUCTION 33 3.2 MATERIALS AND METHODS 34 3.2.1 Bacterial strains 34 3.2.2 Genome sequencing, assembly, and annotation 35 3.2.3 Phylogenetic and comparative analyses 36 3.3 RESULTS 37 3.3.1 Phylogenetic placement of S. Atrichopogonis and S. Eriocheiris 37 3.3.2 Genome features of S. Atrichopogonis and S. Eriocheiris 38 3.3.3 Comparison of gene content and substrate utilization strategies 39 3.3.4 Horizontal gene transfer in S. Eriocheiris 41 3.3.5 Gene acquisition in S. Atrichopogonis mediated by mobile genetic elements 42 3.4 DISCUSSION 44 3.4.1 A model for the molecular evolution events in the mirum clade 44 3.4.2 Other examples of genome degradation in arthropod symbionts 44 3.4.3 Horizontally transferred genes: source, function, and potential link to adaptation 45 3.4.4 Implications on bacterial species description and identification 45 4 Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense 56 4.1 INTRODUCTION 56 4.2 MATERIALS AND METHODS 58 4.2.1 Molecular phylogenetic inference 58 4.2.2 Strain source and DNA preparation 58 4.2.3 Genome sequencing and assembly 59 4.2.4 Annotation and comparative analysis 59 4.3 RESULTS AND DISCUSSION 61 4.3.1 Molecular phylogeny of mosquito-associated Spiroplasma Species 61 4.3.2 Genome sequences of S. Diminutum and S. Taiwanense 62 4.3.3 Comparison of substrate utilization strategies 64 4.3.4 Gene content comparison with the honeybee-associated S. Melliferum 65 4.3.5 Comparison with the Mycoides-Entomoplasmataceae clade and inference of gene content evolution 67 4.4 CONCLUSIONS 68 5 Transcriptome profiling provides insights into the genome evolution and carbohydrate utilization preference of mosquito-associated Spiroplasma 78 5.1 INTRODUCTION 78 5.2 MATERIALS AND METHODS 80 5.2.1 Bacterial strains and growth conditions 80 5.2.2 RNA extraction and transcriptome sequencing 81 5.2.3 Sequence analysis 81 5.2.4 Validation of the RNA-Seq results by qrt-PCR 82 5.2.5 Comparative genomics and molecular phylogenetics 82 5.3 RESULTS AND DISCUSSION 83 5.3.1 Overview of the RNA-Seq data sets 83 5.3.2 The non-coding rnas in S. Diminutum and S. Taiwanense 84 5.3.3 Expression profiles of S. Diminutum 84 5.3.4 Expression profile of S. Taiwanense 86 5.3.5 Gene content evolution in the Apis clade 88 5.3.6 Expression of horizontally acquired genes and the implication on facultative symbiont genome evolution 89 5.4 CONCLUSIONS 90 6 Conclusion 100 7 References 104zh_TW
dc.subjecthorizontal gene transferen_US
dc.subjectfacultative symbiontsen_US
dc.titleGenome evolution in Spiroplasmaen_US
dc.typethesis and dissertationen_US
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item.openairetypethesis and dissertation-
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