Characterization of Rice Genomes and Transcriptomes Using Novel Sequencing Technologies

使用新型测序技术表征水稻基因组和转录组

• 批准号: 0608405
• 负责人: William McCombie
• 金额: --
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0608405&HistoricalAwards=false
• 关键词: Characterization; Rice; Genomes; Transcriptomes; Using

PI: W. Richard McCombie (Cold Spring Harbor Lab)CO-PIs: Li Liao (University of Delaware), Black C. Meyers (University of Delaware) DNA sequencing technology has entered a phase of very rapid change after nearly a decade of slower, incremental changes. In particular, radically different types of sequencers ( e.g. 454 Lifesciences, Solexa) have been developed which have provided large amounts of data but much shorter individual sequence lengths than are provided by current sequencers. The primary goal of this proposal is to (1) test these methods by genomic sequencing of orthologous regions from four rice species (Oryza glaberrima, O. punctata, O. officinalis, and O. minuta) (2) develop new strategies and software tools to most effectively use these new sequencers in combination with previous sequencers. During development and testing of the assembly algorithm, the investigators will assess the assembly of different ratios (mixtures) of coverage from each technology platform. As a result of this project, the investigators will determine the most efficient method to sequence additional important plant genomes in the future using one or a combination of these sequencing technologies.Access to project outcomesSequence data will be incorporated into Gramene (www.gramene.org) and the Oryza Map Alignment Project (www.omap.org). Software will be accessible via http://www.cis.udel.edu/~lliao/.

主持：W. Richard McCombie（冷泉港实验室）合作主持：Li Liao（特拉华大学），Black C. Meyers（特拉华大学）DNA测序技术在经历了近十年缓慢的渐进式变化后，进入了一个非常快速的变化阶段。特别是，已经开发出了完全不同类型的测序仪（例如454 Lifesciences， Solexa），这些测序仪提供了大量数据，但比目前的测序仪提供的单个序列长度短得多。本研究的主要目标是：(1)通过对四种水稻（Oryza glaberrima， O. punctata， O. officinalis和O. minuta）的同源区域进行基因组测序来验证这些方法；(2)开发新的策略和软件工具，以最有效地将这些新测序仪与先前的测序仪结合使用。在组装算法的开发和测试过程中，研究人员将评估来自每个技术平台的不同覆盖比例（混合）的组装。作为这个项目的结果，研究人员将确定未来使用这些测序技术中的一种或组合对其他重要植物基因组进行测序的最有效方法。获取项目成果序列数据将纳入Gramene （www.gramene.org）和Oryza地图比对项目（www.omap.org）。软件将通过http://www.cis.udel.edu/~lliao/访问。