Exploring the Viral Diversity Associated with Wild Rice Plan
发布时间：2023-01-25 22:50
本次研究的核心内容是结合二代测序和生物信息学手段综合分析野生稻中的病毒多样性。水稻是世界上种植最广泛的粮食作物之一,其产量仅次于玉米,位居第二。水稻主产于亚洲国家,大部分南美和中美洲以及一些非洲国家。南亚以及东南亚地区的湿热气候尤其适合水稻的生产,然而,这种独特的气候也适宜感染水稻的病毒和病毒载体的生长。截止目前,文献中已报导的水稻病毒病大约有30种。在过去的几年中,二代测序技术彻底变革了病毒的研究,至今仍是研究病毒多样性的最强有力的手段。在自然界中,病毒无处不在,能感染几乎所有的生命体。而二代测序,可以大范围地检测到病毒的种类。无论是已知病毒还是新病毒都可以在不同的植物样本中被识别和鉴定。病毒病对植物生长来说通常是毁灭性的,对产量造成巨大的损失。然而,大多数病毒的诊断技术都依赖抗原抗体杂交,并要求预先了解致病原。而且,这些技术不能检测到样本中存在的新的病原体。鉴于传统病毒诊断技术的诸多问题和缺陷,二代测序技术的出现成为一种具有替代性的和极具魅力的工具。它不需要预先了解病原体,能更快更准确地鉴别出已知病毒和新病毒。在本次研究中,我们运用宏基因组学的二代测序技术分析鉴别与野生稻相关的病毒...
【文章页数】：131 页
【学位级别】：博士
【文章目录】：
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
【参考文献】：
期刊论文
[1]稻飞虱暴发与南方水稻黑条矮缩病流行的宏观规律和微观机制[J]. 翟保平,周国辉,陶小荣,陈晓,沈慧梅. 应用昆虫学报. 2011(03)
本文编号：3731883
【文章页数】：131 页
【学位级别】：博士
【文章目录】：
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
【参考文献】：
期刊论文
[1]稻飞虱暴发与南方水稻黑条矮缩病流行的宏观规律和微观机制[J]. 翟保平,周国辉,陶小荣,陈晓,沈慧梅. 应用昆虫学报. 2011(03)
本文编号：3731883
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