近年來基因組測序技術(shù)發(fā)展迅速,但基因組的從頭組裝技術(shù)卻依然面臨嚴(yán)峻挑戰(zhàn)�；蚪M從頭組裝技術(shù)中最難攻克的是scaffolds序列的定位及排序問題。在已測序的亞洲棉基因組中,通過遺傳圖譜將3740個(gè)scaffold序列錨定定向到了13條染色體上。然而通過各種序列比對分析如對相近物種的序列進(jìn)行同線性及共線性分析,發(fā)現(xiàn)亞洲棉的基因組測序草圖中存在各種錯誤組裝。為了解決這個(gè)問題,我們利用遺傳圖譜與有參組裝相結(jié)合的方法對亞洲棉A12染色體進(jìn)行了更為精準(zhǔn)的組裝。重新組裝后的亞洲棉A12染色體長達(dá)94.64Mb,包含144個(gè)scaffolds,共計(jì)3361個(gè)蛋白編碼基因。我們發(fā)現(xiàn)在之前的A12染色體組裝過程中,大多數(shù)錯誤組裝發(fā)生在將scaffolds錨定定向到擬染色體上這一步驟上。通過將雷蒙德氏棉和陸地棉中相應(yīng)的染色體與重新組裝的染色體進(jìn)行序列比較分析,如序列共線性同線性以及系統(tǒng)發(fā)生學(xué)分析,結(jié)果證明了重新組裝的染色體在精準(zhǔn)性方面同之前組裝的染色體相比有了質(zhì)的提升。通過系統(tǒng)發(fā)生學(xué)研究,我們還發(fā)現(xiàn)了陸地棉中的Dt₁2染色體與D組祖先雷蒙德氏棉中D12之間的進(jìn)化分歧比At_1<... 

【文章來源】：中國農(nóng)業(yè)科學(xué)院北京市

【文章頁數(shù)】：145 頁

【學(xué)位級別】：博士

【文章目錄】：
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 (參考文獻(xiàn))
ACKNOWLEDGEMENTS (致謝)
CURRICULUM VITAE (作者簡歷)
APPENDIX


【參考文獻(xiàn)】：
期刊論文
[1]亞洲棉石系亞1號耐旱相關(guān)基因SSH文庫的構(gòu)建及其分析[J]. 張玲,李付廣,劉傳亮,張朝軍,武芝霞.  棉花學(xué)報(bào). 2010(02)
[2]Sequencing of a Cultivated Diploid Cotton Genome-Gossypium arboreum[J]. WILKINS Thea A.  棉花學(xué)報(bào). 2008(S1)
[3]ERF轉(zhuǎn)錄因子對生物脅迫的反應(yīng)及對棉花抗性改良的意義[J]. 孟憲鵬,李付廣,劉傳亮,張朝軍,武芝俠.  分子植物育種. 2008(01)



本文編號：3431230