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

SGER：使用 SOLiD 测序平台开发小麦 BAC 从头测序的新策略

• 批准号: 0840615
• 负责人: Jan Dvorak
• 金额: $ 19.6万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0840615&HistoricalAwards=false
• 关键词: SGER; Development; Novel; Strategy; De

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.

首席研究员：Jan Dvorak（加州大学戴维斯分校） 首席研究员：Katrien M. Devos（佐治亚大学）、Olin D. Anderson 和 Ming-Cheng Luo（加州大学戴维斯分校） 目前，对大型植物基因组（例如小麦、大麦和其他重要经济植物）进行完整的 BAC-by-BAC 测序的成本过高。下一代测序技术，例如 454 Life Sciences (Roche)、Solexa (Illumina) 和 SOLiD (Applied BioSystems)，可提供更高吞吐量和大幅降低成本的测序。不幸的是，短读长使得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尤其如此。该项目的目标是与 Applied BioSystems 合作，评估使用 SOLiD 平台进行从头测序的新策略。该策略将采用基因组 DNA 细菌人工染色体 (BAC) 克隆的二维库进行测序。该策略将使用节节山羊草 BAC 克隆的二维池进行评估，节节山羊草是多倍体小麦的二倍体祖先之一。将编写一个程序来对池进行解卷积并组装单个克隆的序列。 更广泛的影响：为 SOLiD 测序平台开发从头测序策略将使认真考虑以现实的成本和现实的时间框架对具有大基因组的物种（例如小麦）进行基因组测序成为可能。希望所开发的测序技术和软件能够普遍适用于任何大型植物基因组的测序。公众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，例如 GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml)，该网站提供小麦和其他谷物的分子和表型信息汇编。