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

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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