| ACKNOWLEDGEMENTS | 第1-8页 |
| ABSTRACT | 第8-11页 |
| 中文摘要 | 第11-13页 |
| CHAPTER 1 INTRODUCTION | 第13-17页 |
| ·GENERAL INTRODUCTION | 第13-15页 |
| ·OBJECTIVES OF THE STUDY | 第15-16页 |
| ·OVERVIEW OF THE STUDY | 第16-17页 |
| CHAPTER 2 LITERATURE REVIEW | 第17-31页 |
| ·MECHANISM OF HORIZONTAL GENE TRANSFER | 第17-21页 |
| ·Transformation | 第17-18页 |
| ·Transduction | 第18-20页 |
| ·Conjugation | 第20-21页 |
| ·BARRIERS TO HGT BETWEEN BACTERIA | 第21-24页 |
| ·Restriction as barrier | 第22-23页 |
| ·Surface exclusion as a barrier | 第23-24页 |
| ·HORIZONTAL GENE TRANSFER IN PROKARYOTES AND EUKARYOTES | 第24-26页 |
| ·Horizontal gene transfer in prokaryotes | 第24-25页 |
| ·Horizontal gene transfer in eukaryotes | 第25-26页 |
| ·EXISTING METHODS FOR DETECTING HORIZONTAL GENE TRANSFER | 第26-31页 |
| ·Comparing phylogenetic trees of different genes | 第27-28页 |
| ·Anomalous nucleotide composition | 第28页 |
| ·Conservation of gene order between distant taxa | 第28-29页 |
| ·Unexpected ranking of sequence similarity among homologs | 第29-31页 |
| CHAPTER 3 CGS:A NEW COMPUTATIONAL METHOD FOR THE DETECTION OF LATERAL GENE TRANSFER EVENTS | 第31-56页 |
| ·INTRODUCTION | 第31-32页 |
| ·METHODS | 第32-38页 |
| ·Overview | 第32-33页 |
| ·Determination of core genes used as the reference set | 第33页 |
| ·Determination of set of underrepresented oligonucleotides | 第33-34页 |
| ·Computation of scores of merit and threshold values | 第34-35页 |
| ·Calculations using existing methods | 第35-36页 |
| ·Sampling experiments | 第36-38页 |
| ·RESULT | 第38-53页 |
| ·Preliminary tests of parameters of the standard method | 第38-50页 |
| ·Choice of oligonucleotide length | 第38-39页 |
| ·Choice of reference set | 第39-40页 |
| ·Choice of statistical tests to assess deviance of gene from reference set | 第40-44页 |
| ·Choice of the threshold of underrepresented oligonucleotides | 第44-46页 |
| ·Choice of the percent of core genes in reference set | 第46页 |
| ·Power to detect genes from organisms of different evolutionary distances | 第46-48页 |
| ·Establishment of appropriate threshold | 第48-50页 |
| ·Comparison of the standard method with existing methods to detect foreign genes by simulation | 第50-52页 |
| ·Comparison of the standard method with different methods to detect foreign genes by phylogenetic tree | 第52-53页 |
| ·DISCUSSION | 第53-56页 |
| CHAPTER 4 MGC:IDENTIFICATION OF GENOMIC ISLANDS IN PROCHLOROCOCCUS MED4 BY 5 CYANOBACTERIA GENOMES COMPARISON | 第56-82页 |
| ·INTRODUCTION | 第56-58页 |
| ·METHODS | 第58-60页 |
| ·Definition of genomic island | 第58页 |
| ·Construction of phylogenetic tree and identification of orthologs | 第58-59页 |
| ·Detection of putative genomic islands | 第59页 |
| ·Search for the homologs of alien genes in NCBI | 第59页 |
| ·Search for the homologs of alien genes in phages and virus | 第59-60页 |
| ·RESULT | 第60-80页 |
| ·Standard phylogenetic tree | 第60-61页 |
| ·Ortholog of PMED4 genes among PMC,PMB,PMG,PMI | 第61页 |
| ·Putative alien genes in PMED4 | 第61-64页 |
| ·Genomic islands position characteristics | 第64-68页 |
| ·tRNA associated with genomic islands is insertion hot spot | 第68-69页 |
| ·Codon usage corresponding to tRNA associated with GI among GI and Genome | 第69-76页 |
| ·Transfer of PMED4 alien genes to and from phages | 第76-80页 |
| ·DISCUSSION | 第80-82页 |
| REFERENCES | 第82-96页 |
