声明
摘要
Abstract
Table of Contents
List of Tables
List of Figures
List of Appendix
Abbreviations
CHAPTER 1 INTRODUCTION
1．1 Introduction of cotton
1．1．1 Cotton usage and consumption
1．1．2 Taxonomy and history of cotton
1．1．3 Genome size variations within the genus Gossypium
1．2 Sequencing of cotton genome
1．3 Recent advances in cotton genome sequencing(review)
1．3．1 Sequencing of diploid cotton genomes
1．3．2 Sequencing of tetraploid cotton genomes
1．3．3 Re-sequencing of different cotton species
1．4 De novo assembling of sequenced plant genome
1．4．1 Current challenges in plant genome assembly
1．4．2 Mis-assemblies in sequenced genomes
1．5 Mis-assemblies in sequenced cotton genomes
1．6 Reference assisted chromosome assembly
1．7 Comparative genomies
1．7．1 Comparative analysis of different cotton genomes(Review)
Objectives of Research
CHAPTER 2 MATERIALS AND METHODS
2．1 Genome data of different cotton species
2．2 Assembling of G．arboreum chromosome 12 by genetic map
2．2．1 Good quality marker selection
2．2．2 Construction of linkage groups
2．2．3 Assignment of chromosome names to linkage groups
2．3 Assembling of G．arboreum chromosome 12 by reference assisted approach
2．3．1 Alignment with G．raimondii scaffolds
2．3．2 Alignment with G．raimondii and G．hirsutum chromosomes
2．4 Further correction of chromosome assembly
2．5 Final assembling of G．arboreum chromosome
2．6 Gene content of G．arboreum Chromosome 12
2．7 Identification of orthologous genes
2．8 Evolution analysis
2．9 Collinear and syntenic relationship
2．9．1 BLASTP search
2．9．2 Commands for MCSeanX
2．9．3 Classification of duplicate genes
2．9．4 Construction of dot plots
2．9．5 Construction of dual synteny plotter
2．9．6 Construction of circle plotter
2．9．7 Construction of bar plotter
2．11 Identification of TF-related gene families
2．13 Chromosomal distribution of TF-related genes
CHAPTER 3 RESULTS
3．1．1 Construction of genetic map for re-assembling
3．1．2 Reference assisted approach for re-assembling
3．2．Gene content of G．arboreum chromosome 12
3．2．1 Identification of TF-related genes in G．arboreum chromosome 12
3．3．Evidences for improved assembly of G．arboreum chromosome
3．3．1 Collinearity and synteny analysis
3．3．2 Evolution analysis
3．4 Comparative analysis among chromosomes of different cotton species
3．4．1 Putative gene loss events
3．4．2 Phylogenetie analysis of transcription factor related genes
3．4．3 Chromosomal distribution of transcription factor related genes
CHAPTER 4 DISCUSSION
4．1．1 Size of re-assembled G．arboreum chromosome 12
4．1．2 Gene content within G．arboreum chromosome 12
4．2．1 N50 for the anchored and oriented scaffolds
4．2．3 Synteny and collinearity with the previous G．arboreum chromosome
4．2．4．Evolution analysis
4．3 Comparative analysis among chromosomes of different cotton species
4．3．2 Phyiogenetie analysis among TF-related genes
4．3．3 Physical mapping of TF-related genes
Conclusion
References
Acknowledgements
Curriculum Vitae
APPENDIX
