SGER: Development of a Novel Strategy for De Novo Sequencing of Wheat BACs Using the SOLiD Sequencing Platform

Pi：Jan Dvorak(加州大学戴维斯分校)Copis：Kateen M.Devos(佐治亚大学)、Olin D.Anderson和Luing-cheng Luo(加州大学戴维斯分校)完成大型植物基因组的BAC-by-BAC测序，如小麦、大麦和其他重要的经济植物的基因组，目前成本高得令人望而却步。下一代测序技术，如454生命科学(罗氏)、Solexa(Illumina)和Solid(应用生物系统)，提供了更高的产量和更低的成本。不幸的是，短的阅读长度使这些技术在真核基因组从头测序中的使用变得复杂。对于包含大量重复DNA序列的大型植物基因组来说，情况尤其如此。该项目的目标是与应用生物系统公司合作，评估使用Solid平台进行从头测序的新战略。这一策略将利用基因组DNA的细菌人工染色体(BAC)克隆的二维池进行测序。这一策略将使用多倍体小麦的二倍体祖先之一节节麦的BAC克隆的二维池进行评估。将编写一个程序来解卷这些池并组装单个克隆的序列。广泛的影响：为固体测序平台开发从头测序策略将使以现实的成本和现实的时间框架认真考虑具有大基因组的物种(如小麦)的基因组测序成为可能。希望所开发的测序技术和软件将普遍适用于任何大的植物基因组的测序。用于公开访问所开发的汇编软件的初始存储库位于http://wheatdb.ucdavis.edu:8080/wheatdb/index.jsp.该软件还将与公共网站集成，如GrainGenes(http://wheat.pw.usda.gov/GG2/index.shtml)，)，它提供了关于小麦和其他谷物的分子和表型信息的汇编。

PI: Jan Dvorak (University of California - Davis)CoPIs: Katrien M. Devos (University of Georgia), Olin D. Anderson and Ming-Cheng Luo (University of California - Davis)Complete BAC-by-BAC sequencing of large plant genomes, such as those of wheat, barley, and other economically important plants, is currently prohibitively expensive. Next generation sequencing technologies, such as the 454 Life Sciences (Roche), Solexa (Illumina), and SOLiD (Applied BioSystems), offer sequencing with much higher throughputs and at greatly reduced costs. Unfortunately, the short read-lengths complicate the use of these techniques in de novo sequencing of eukaryotic genomes. That is particularly true for large plant genomes that contain vast amounts of repeated DNA sequences. The goal of this project is to assess a novel strategy for de novo sequencing with the SOLiD platform in collaboration with Applied BioSystems. This strategy will employ sequencing of two-dimensional pools of bacterial artificial chromosome (BAC) clones of genomic DNA. The strategy will be evaluated using two-dimensional pools of BAC clones of Aegilops tauschii, one of the diploid ancestors of polyploid wheat. A program will be written to deconvolute the pools and assemble sequences of individual clones.Broader impacts: The development of a de novo sequencing strategy for the SOLiD sequencing platform will make it possible to seriously consider genome sequencing of species with large genomes, such as wheat, at realistic costs and in a realistic time frame. It is the hope that the sequencing technique and the software developed will be universally applicable to the sequencing of any large plant genome. The initial repository for public access to the assembly software developed is at http://wheatdb.ucdavis.edu:8080/wheatdb/index.jsp. The software will also be integrated with public web sites, such as GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml), that provides a compilation of molecular and phenotypic information on wheat and other cereals.