亚洲棉12号染色体的重组装及比较分析揭示亚洲棉基因组染色体水平的错误组装

发布时间：2021-10-11 20:59

　　近年来基因组测序技术发展迅速,但基因组的从头组装技术却依然面临严峻挑战。基因组从头组装技术中最难攻克的是scaffolds序列的定位及排序问题。在已测序的亚洲棉基因组中,通过遗传图谱将3740个scaffold序列锚定定向到了13条染色体上。然而通过各种序列比对分析如对相近物种的序列进行同线性及共线性分析,发现亚洲棉的基因组测序草图中存在各种错误组装。为了解决这个问题,我们利用遗传图谱与有参组装相结合的方法对亚洲棉A12染色体进行了更为精准的组装。重新组装后的亚洲棉A12染色体长达94.64Mb,包含144个scaffolds,共计3361个蛋白编码基因。我们发现在之前的A12染色体组装过程中,大多数错误组装发生在将scaffolds锚定定向到拟染色体上这一步骤上。通过将雷蒙德氏棉和陆地棉中相应的染色体与重新组装的染色体进行序列比较分析,如序列共线性同线性以及系统发生学分析,结果证明了重新组装的染色体在精准性方面同之前组装的染色体相比有了质的提升。通过系统发生学研究,我们还发现了陆地棉中的Dt₁2染色体与D组祖先雷蒙德氏棉中D12之间的进化分歧比At_1<... 

【文章来源】：中国农业科学院北京市

【文章页数】：145 页

【学位级别】：博士

【文章目录】：
摘要
Abstract
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 genomics
        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 MCScan X
        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
    2.10 Gene loss
    2.11 Identification of TF-related gene families
    2.12 Phylogenetic analysis of TF-related genes
    2.13 Chromosomal distribution of TF-related genes
CHAPTER 3 RESULTS
    3.1. Re-assembling of G. arboreum chromosome 12
        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 Phylogenetic analysis of transcription factor related genes
        3.4.3 Chromosomal distribution of transcription factor related genes
CHAPTER 4 DISCUSSION
    4.1 Re-assembling of G. arboreum chromosome 12
        4.1.1 Size of re-assembled G. arboreum chromosome 12
        4.1.2 Gene content within G. arboreum chromosome 12
    4.2 Evidences for improved assembly of G. arboreum chromosome
        4.2.1 N50 for the anchored and oriented scaffolds
        4.2.2 Synteny and collinearity with the chromosomes of different cotton species
        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
        4.3.1 Gene loss
        4.3.2 Phylogenetic analysis among TF-related genes
        4.3.3 Physical mapping of TF-related genes
CONCLUSION
REFERENCES (参考文献)
ACKNOWLEDGEMENTS (致谢)
CURRICULUM VITAE (作者简历)
APPENDIX


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期刊论文
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