Applications of Ultra-high-Throughput Sequencing
Applications of Ultra-high-Throughput Sequencing
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DOI：
10.1007/978-1-60327-563-7_5
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发表时间：
2009-01-01
期刊：
影响因子：
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通讯作者：
Mockler, Todd C.
中科院分区：
文献类型：
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作者：
Fox, Samuel;Filichkin, Sergei;Mockler, Todd C.
基因组学时代使科学家能够更容易地提出关于突变、进化、基因和基因组结构、功能和调控的真正全球性问题。正如桑格测序带来了范式转变，使生物学问题的分子基础能够直接得到解决一样，超高通量DNA测序也将在更大程度上极大地改变生物学研究的性质。新的测序技术为在比较基因组学、系统生物学、宏基因组学和基因组生物学领域的整个基因组水平上解决新问题打开了大门。与桑格测序相比，这些新的测序技术以惊人的速度提供了大量的DNA序列数据，并且降低了成本、工作量和时间。超高通量测序（UHTS）的应用基本上仅受研究人员想象力的限制，包括基因组测序/重测序、小RNA发现、深度SNP发现、染色质免疫沉淀（ChIP）和RNA免疫沉淀（RIP）与序列鉴定、转录组分析（包括经验注释）、选择性剪接的发现和表征以及基因表达谱分析。这项技术将对植物育种、生物技术以及我们对植物进化、发育和环境反应的基本理解产生深远的影响。在本章中，我们提供了一个概述UHTS方法及其应用。我们还描述了一个协议，我们已经开发的植物转录组的深度测序使用Illunina/Solexa测序平台。
The genomics era has enabled scientists to more readily pose truly global questions regarding mutation, evolution, gene and genome structure, function, and regulation. Just as Sanger sequencing ushered in a paradigm shift that enabled the Molecular basis of biological questions to be directly addressed, to an even greater degree, ultra-high-throughput DNA sequencing is poised to dramatically change the nature of biological research. New sequencing technologies have opened the door for novel questions to be addressed at the level of the entire genome in the areas of comparative genomics, systems biology, metagenomics, and genome biology. These new sequencing technologies provide a tremendous amount of DNA sequence data to be collected at an astounding pace, with reduced costs, effort, and time as compared to Sanger sequencing. Applications of ultra-high-throughput sequencing (UHTS) are essentially limited only by the imaginations of researchers, and include genome sequencing/resequencing, small RNA discovery, deep SNP discovery, chromatin immunoprecipitation (ChIP) and RNA immunoprecipitation (RIP) coupled with sequence identification, transcriptome analysis including empirical annotation, discovery and characterization of alternative splicing, and gene expression profiling. This technology will have a profound impact on plant breeding, biotechnology, and our fundamental understanding of plant evolution, development, and environmental responses. In this chapter, we provide an overview of UHTS approaches and their applications. We also describe a protocol we have developed for deep sequencing of plant transcriptomes using the Illunina/Solexa sequencing platform.