本次研究的核心內(nèi)容是結(jié)合二代測(cè)序和生物信息學(xué)手段綜合分析野生稻中的病毒多樣性。水稻是世界上種植最廣泛的糧食作物之一,其產(chǎn)量僅次于玉米,位居第二。水稻主產(chǎn)于亞洲國家,大部分南美和中美洲以及一些非洲國家。南亞以及東南亞地區(qū)的濕熱氣候尤其適合水稻的生產(chǎn),然而,這種獨(dú)特的氣候也適宜感染水稻的病毒和病毒載體的生長。截止目前,文獻(xiàn)中已報(bào)導(dǎo)的水稻病毒病大約有30種。在過去的幾年中,二代測(cè)序技術(shù)徹底變革了病毒的研究,至今仍是研究病毒多樣性的最強(qiáng)有力的手段。在自然界中,病毒無處不在,能感染幾乎所有的生命體。而二代測(cè)序,可以大范圍地檢測(cè)到病毒的種類。無論是已知病毒還是新病毒都可以在不同的植物樣本中被識(shí)別和鑒定。病毒病對(duì)植物生長來說通常是毀滅性的,對(duì)產(chǎn)量造成巨大的損失。然而,大多數(shù)病毒的診斷技術(shù)都依賴抗原抗體雜交,并要求預(yù)先了解致病原。而且,這些技術(shù)不能檢測(cè)到樣本中存在的新的病原體。鑒于傳統(tǒng)病毒診斷技術(shù)的諸多問題和缺陷,二代測(cè)序技術(shù)的出現(xiàn)成為一種具有替代性的和極具魅力的工具。它不需要預(yù)先了解病原體,能更快更準(zhǔn)確地鑒別出已知病毒和新病毒。在本次研究中,我們運(yùn)用宏基因組學(xué)的二代測(cè)序技術(shù)分析鑒別與野生稻相關(guān)的病毒... 

【文章頁數(shù)】：131 頁

【學(xué)位級(jí)別】：博士

【文章目錄】：
ACKNOWLEDGEMENT ABSTRACT 摘要 LIST OF ABBREVIATIONS CHAPTER 1 Introduction
1.1 Emerging plant viruses
1.2 Rice production and its susceptibility to viral infection
1.3. General characteristics of rice viruses
1.4. Viral Diversity Associated with Rice
    Rice Black-Streaked Dwarf Virus
    Southern rice black-streaked dwarf virus
    Rice grassy stunt virus
    Rice ragged stunt virus
    Rice stripe virus
    Rice hoja blanca tenuivirus
    Rice dwarf virus
    Rice gall dwarf virus
    Rice stripe necrosis virus
    Rice necrosis mosaic virus
    Rice stripe mosaic virus
    Rice yellow stunt virus
    Rice tungro bacilliform & spherical virus
    Rica virus A
    Rice yellow mottle virus
1.5. Diagnosis of rice infecting viruses
    ELISA
    Latex agglutination reaction
    MULTIPLEX RT-PCR
    RT-LAMP
    REAL-TIME RT-PCR
1.6. Next-Generation High Throughput Sequencing and plant viruses' discovery
    NGS and the Discovery of Novel Viruses
    Ecogenomics of Viruses
    Complete Genome Sequencing
    Study of Antiviral Defense Mechanism
1.7. Dissertation outline CHAPTER 2 Materials and Method
2.1. Study Samples
2.2. Total RNA Extraction
2.3. Small RNA library preparation and sequencing
2.4. RNA library preparation and sequencing
2.5. Bioinformatics analysis
    2.5.1. Mapping of sequencing data
    2.5.2. Bowtie and Bowtie2
    2.5.3. SAM and BAM files format
    2.5.4. Visualization of genomic data
    2.5.5. De novo genome assembly
    2.5.6. Velvet
    2.5.7. Oases
    2.5.8. Metavelvet
    2.5.9. Trinity
    2.5.10. Seqman
2.6. Validation and confirmation of assembled genomes by RT-PCR CHAPTER 3 Identification of known and novel viral sequences identified in this study
3.1. Summary of the assembled sequencing data generated from 100 rice plants samples
    3.1.1. Prevalence and abundance of known viruses identified in wild rice samples
    3.1.2. Prevalence and abundance of new viruses identified in wild rice samples
3.2. Identification and characterization of rice infecting viruses
    3.2.1. Rice grassy stunt tenuivirus
    3.2.2. Rice ragged stunt virus
    3.2.3. Rice gall dwarf virus
    3.2.4. Southern rice black-streaked dwarf virus (SRBSDV)
    3.2.5. Oryza sativa alphaendornavirus
    3.2.6. Discussion
3.3. Identification and characterization of novel poleroviruses associated with Wild RicePlants
    3.3.1. Summary
    3.3.2 Background
    3.3.3 Materials and Methods
    3.3.4. Results
    3.3.5. Discussion CHAPTER 4 Conclusions and future perspectives References Appendix


【參考文獻(xiàn)】：
期刊論文
[1]稻飛虱暴發(fā)與南方水稻黑條矮縮病流行的宏觀規(guī)律和微觀機(jī)制[J]. 翟保平,周國輝,陶小榮,陳曉,沈慧梅.  應(yīng)用昆蟲學(xué)報(bào). 2011(03)



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