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

PI：Jan Dvorak（加州-戴维斯大学）CoPI：Katrien M. Devos（格鲁吉亚大学），Olin D.安德森和Ming-Cheng Luo（加州-戴维斯大学）大型植物基因组（如小麦、大麦和其他经济上重要的植物）的完整BAC-by-BAC测序目前非常昂贵。下一代测序技术，如454 Life Sciences（Roche）、Solexa（Illumina）和SOLiD（Applied BioSystems），提供具有高得多的通量和大大降低的成本的测序。不幸的是，短的读取长度使这些技术在真核基因组的从头测序中的使用复杂化。对于含有大量重复DNA序列的大型植物基因组来说，情况尤其如此。该项目的目标是评估与Applied BioSystems合作的SOLiD平台进行从头测序的新策略。该策略将采用基因组DNA的细菌人工染色体（BAC）克隆的二维池的测序。该策略将使用节节麦（多倍体小麦的二倍体祖先之一）的BAC克隆的二维池进行评估。更广泛的影响：SOLiD测序平台的从头测序策略的发展将使人们有可能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。希望测序技术和开发的软件将普遍适用于任何大型植物基因组的测序。供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GrainGenes（http：//wheat.tag.usda.gov/GG2/index.shtml）等公共网站结合，提供小麦和其他谷物的分子和表型信息汇编。

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.