ABI Innovation: Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing

ABI 创新：无条形码多重分析：利用组合池进行高通量测序

• 批准号: 1062301
• 负责人: Stefano Lonardi
• 金额: $ 42.06万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-05-01 至 2015-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1062301&HistoricalAwards=false
• 关键词: ABI; Innovation; Barcoding; Free; Multiplexing

The University of California, Riverside is awarded a grant to developan innovative sequencing protocol for hierarchical (i.e., BAC-by-BAC)genome sequencing of large eukaryotic genomes. At the core of theprotocol is the ability to solve a set of hard computationalquestions, which are the focus of the research plan. The computationalchallenges require the study of novel combinatorial optimizationproblems, the development of innovative time- and space-efficientalgorithms, and ultimately the implementation and deployment ofuser-friendly web-based software tools. The new combinatorialsequencing protocol is going to be tested to the cowpea genome. CowpeaVigna unguiculata, also known as China bean or black-eyed pea,is one of the most important food legume crops in the semi-aridtropics covering Asia, Africa, and Central and South America. Adrought-tolerant and warm-weather crop, cowpeas are well-adapted tothe drier regions of the tropics, where other food legumes do notperform well. Its modest genome size makes it an excellent candidateto demonstrate the utility of our protocol. We expect the finalassembly to provide a sufficient depth of knowledge to support mostdownstream applications including map-based cloning of traitdeterminants, development of markers for marker-assisted breeding,microarray development for gene expression studies and analysis ofsynteny with related species.This project will advance sequencing techniques for complex genomes,using cowpea, an essential food source in developingcountries. Software tools and the assembled data will be placed intothe public domain, which will benefit researchers and the publicworldwide, and potentially lead to new international and industrialcollaborations. This project will directly support one graduatestudents in a highly interdisciplinary environment, building on UCR'sstrengths in Computer Science and AgriculturalSciences. Undergraduates will have opportunities to participate inresearch through a Research Experiences for Undergraduates (REU) siteat UCR, a collaboration with a nearby community college, and a new USDepartment of Education Title V Hispanic Serving Institution grant(UCR is an accredited HSI).More details and information about this project will be available athttp://www.cs.ucr.edu/~stelo/dbi.htm

加州大学，滨江被授予一笔赠款，以开发一种创新的测序方案，用于分层（即，大的真核基因组的BAC-by-BAC）基因组测序。该协议的核心是解决一系列困难的计算问题的能力，这是研究计划的重点。计算的挑战需要研究新的组合优化问题，开发创新的时间和空间效率的算法，并最终实现和部署用户友好的基于Web的软件工具。 新的组合测序方案将在豇豆基因组上进行测试。豇豆（Vigna unguiculata），又名中国豆或黑眼豆，是亚洲、非洲和中南美洲半干旱热带地区最重要的食用豆类作物之一。豇豆是一种耐旱、气候温暖的作物，很好地适应了热带干旱地区，在那里其他食用豆类表现不佳。 其适度的基因组大小使其成为展示我们方案实用性的绝佳候选者。我们希望最终的组装能够提供足够的知识深度，以支持大多数下游应用，包括性状决定因子的图位克隆、标记辅助育种的标记开发、基因表达研究的微阵列开发以及与相关物种的同线性分析。该项目将推进复杂基因组的测序技术，使用豇豆，这是发展中国家的一种重要食物来源。软件工具和收集的数据将被置于公共领域，这将使全世界的研究人员和公众受益，并可能导致新的国际和工业合作。这个项目将直接支持一个研究生在一个高度跨学科的环境，在计算机科学和计算机科学的UCR的优势建设。本科生将有机会通过UCR的本科生研究经验（REU）网站参与研究，与附近的社区学院合作，以及新的美国教育部第五章西班牙裔服务机构补助金（UCR是一个认可的HSI）。有关该项目的更多细节和信息将在http：//www.example.com上提供www.cs.ucr.edu/~stelo/dbi.htm