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

加州大学河滨分校获得了一项资助，用于开发一种创新的测序方案，用于对大型真核生物基因组进行分层（即BAC-by-BAC）基因组测序。该协议的核心是解决一组硬计算问题的能力，这是研究计划的重点。计算挑战要求研究新的组合优化问题，开发创新的时间和空间效率算法，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（copeavigna unguiculata），又称豇豆或黑眼豆，是覆盖亚洲、非洲和中南美洲的半干旱地区最重要的食用豆类作物之一。作为一种耐旱和温暖气候的作物，豇豆很好地适应了热带干旱地区，而其他食用豆类在那里表现不佳。其适度的基因组大小使其成为展示我们的方案效用的绝佳候选者。我们期望最终组装能够提供足够深度的知识来支持大多数下游应用，包括基于图谱的性状决定因子克隆，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源性分析。该项目将利用豇豆（发展中国家的一种重要食物来源）推进复杂基因组测序技术。软件工具和汇编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，并有可能导致新的国际和工业合作。该项目将在一个高度跨学科的环境中直接支持一名研究生，以UCR在计算机科学和农业科学方面的优势为基础。本科生将有机会通过UCR的本科生研究经验（REU）站点，与附近的社区学院合作，以及新的美国教育部标题V西班牙裔服务机构补助金（UCR是一个经过认证的HSI）参与研究。有关该项目的更多细节和信息，请访问：//www.cs.ucr.edu/~stelo/dbi.htm

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