Structural genome annotation and quantification of transcripts based on ultra-high-throughput transcriptome sequencing

基于超高通量转录组测序的结构基因组注释和转录本定量

• 批准号: 179180132
• 负责人: Professor Dr. Mario Stanke
• 金额: --
• 依托单位: Lehrstuhl für Bioinformatik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2010
• 资助国家: 德国
• 起止时间: 2009-12-31 至 2013-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/179180132?language=en
• 关键词: Structural; genome; annotation; quantification; transcripts

New ultra-high throughput sequencing technologies allow much cheaper and deeper sequencing of eukaryotic transcriptomes, termed RNA-Seq. The project aims at developing methods and software tools for the identification of complete transcript sets of protein-coding genes based on RNA-Seq and their accurate quantification in RNA-Seq samples. Based on one of the currently most accurate gene finders, AUGUSTUS, a strucural genome annotation pipeline will be developed that exploits RNA-Seq data simultaneously with other evidence sources. The aim is to generally and significantly increase the accuracy and comprehensiveness of structural genome annotation and to identify alternative splice forms more sensitively and confidently. Expression levels of transcripts will be estimated accurately to allow for the detection of changes in expression of genes or splice variants under different conditions. The universally applicable annotation pipeline will integrate RNA-Seq data from all new sequencing platforms and be freely available for independent use but will also be applied directly in some genome projects. If successful, this project would allow a significantly more accurate annotation and expression analysis in many eukaryotic genomes. It will therefore provide a better basis for other studies with potential biomedical, biotechnological or agricultural applications.

新的超高通量测序技术可以对真核转录组进行更便宜、更深入的测序，称为RNA-Seq。该项目旨在开发方法和软件工具，用于基于RNA-Seq识别蛋白质编码基因的完整转录本集，并在RNA-Seq样品中对其进行准确定量。基于目前最准确的基因发现者之一AUGUSTUS，将开发一个结构基因组注释管道，同时利用RNA-Seq数据和其他证据来源。其目的是普遍和显着提高结构基因组注释的准确性和全面性，并确定选择性剪接形式更敏感和自信。将准确估计转录物的表达水平，以允许检测不同条件下基因或剪接变体表达的变化。普遍适用的注释管道将整合来自所有新测序平台的RNA-Seq数据，并可免费独立使用，但也将直接应用于一些基因组项目。如果成功，该项目将允许在许多真核基因组中进行更准确的注释和表达分析。因此，它将为具有潜在生物医学、生物技术或农业应用的其他研究提供更好的基础。

项目成果

Finding the missing honey bee genes: lessons learned from a genome upgrade

• DOI: 10.1186/1471-2164-15-86
• 发表时间: 2014-01-30
• 期刊: BMC GENOMICS
• 影响因子: 4.4
• 作者: Elsik, Christine G.;Worley, Kim C.;Gibbs, Richard A.
• 通讯作者: Gibbs, Richard A.

Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots.

• DOI: 10.1111/nph.12671
• 发表时间: 2014-04
• 期刊: The New phytologist
• 作者: Van-Tuan Tran;S. Braus-Stromeyer;H. Kusch;Michael Reusche;A. Kaever;Anika Kühn;O. Valerius;Manuel Lan