After the Sequencing: Curating the Medicago Truncatula Genome

测序后：整理蒺藜苜蓿基因组

• 批准号: 0821966
• 负责人: Christopher Town
• 金额: $ 375.98万
• 依托单位: J. Craig Venter Institute, Inc.
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-15 至 2014-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0821966&HistoricalAwards=false
• 关键词: After; Sequencing; Curating; Medicago; Truncatula

PI: Christopher D. Town, J. Craig Venter Institute, Inc.Co-PI: David C. Schwartz, University of WisconsinMedicago truncatula, a close relative of alfalfa, is the preeminent model for legume genomics and has been the target of an international sequencing initiative for the past five years. When the international sequencing efforts wind down in the fall of 2008, there will be ~280 Mb of high quality DNA sequence distributed across the plant's eight chromosomes each with blocks of sequence ranging in size from a few hundred thousand bases to between five and 10 million bases in length and with from 10-30 gaps in each of the euchromatic arms. Based upon the projected capture rate of expressed sequence tags, the euchromatic, gene-rich portion of genome will be around 80% complete. There will also be ~200 Mb of unsequenced DNA in the centromeres that is gene poor and was not targeted for sequencing. This project will integrate, manage and enhance our understanding of both the structure and annotation of the Medicago genome, and comprises three goals:1. Creation of the best possible sequence-based representation of the M. truncatula genome. This will involve construction of an optical map, which is a physical scaffold derived by methods totally independent of the DNA sequencing process. The map will allow the runs of contiguous stretches of DNA sequence (contigs) produced by the sequencing centers to be placed in the correct order and orientation and the sizes of gaps between these contigs and the location and sizes of the gene-poor centromeric regions to be determined.2. Capturing and localizing as much as possible of the remaining gene-containing regions of M. truncatula genome in the most cost-efficient fashion, thus providing a close to complete inventory of its gene content.3. Supporting and maintaining the IMGAG (International Medicago Genome Annotation Group) annotation pipeline that represents a consensus annotation process for the entire Medicago (and legume) community and enriching the annotation of the M. truncatula genome by overlaying other data types including expression data (both microarray and NextGeneration sequencing), proteomic data, locations of transposon and fast-neutron induced mutations, links to genetic resources, etc. With the sequencing projects terminating, members of the IMGAG consortium (including the JCVI group in the US) will have few resources to devote to continued annotation. This project will maintain and keep updated both the sequence content and annotation of the Medicago genome and provide a critical central and stable resource for legume researchers for years to come. The project will also host a community annotation portal that will allow researchers to enrich the basically automatic, computer-generated annotation with more refined structural and functional details based upon their own knowledge and experience. All information generated by this project will be freely accessible through the project web site maintained at the J. Craig Venter Institute (http://www.jcvi.org/cms/research/projects/medicago-truncatula-database/overview/).The project will be monitored by an advisory committee composed of members of the community-elected International Medicago Steering Committee. At the educational level, both participating institutions will host visiting students in their laboratories for summer internships. In addition, annual workshops will be held to provide education in genome annotation and analysis to graduate students, postdoctoral fellows and interested faculty in the legume community.

PI：Christopher D.克雷格文特尔研究所，联合PI：大卫C。蒺藜苜蓿是苜蓿的近亲，是豆科植物基因组学的杰出模型，在过去的五年里一直是国际测序计划的目标。当国际测序工作在2008年秋季结束时，将有~280 Mb的高质量DNA序列分布在植物的八条染色体上，每条染色体的序列块的大小从几十万个碱基到500万到1000万个碱基不等，每条常染色质臂中有10-30个空位。基于表达序列标签的预计捕获率，基因组的常染色质、基因丰富部分将完成约80%。在着丝粒中还将存在约200 Mb的未测序DNA，其是基因贫乏的并且未被靶向用于测序。该项目将整合，管理和提高我们对苜蓿基因组结构和注释的理解，包括三个目标：1。创建M的最佳可能的基于序列的表示。蒺藜基因组这将涉及光学图谱的构建，光学图谱是通过完全独立于DNA测序过程的方法获得的物理支架。该图谱将允许测序中心产生的DNA序列的连续延伸（重叠群）的运行以正确的顺序和方向放置，并且确定这些重叠群之间的间隙的大小和基因贫乏的着丝粒区域的位置和大小。尽可能多地捕获和定位M.以最具成本效益的方式，从而提供了一个接近完整的清单，其基因内容。支持和维护IMGAG（国际苜蓿基因组注释组）注释管道，该管道代表整个苜蓿（和豆类）社区的共识注释过程，并丰富了M.通过覆盖其他数据类型，包括表达数据（微阵列和NextGeneration测序）、蛋白质组学数据、转座子和快中子诱导突变的位置、遗传资源的链接等，IMGAG联盟的成员（包括美国的JCVI组）将几乎没有资源用于继续注释。该项目将维护和更新苜蓿基因组的序列内容和注释，并为豆科植物研究人员提供关键的核心和稳定的资源。该项目还将主办一个社区注释门户网站，使研究人员能够根据自己的知识和经验，用更精细的结构和功能细节丰富基本上自动的计算机生成的注释。该项目产生的所有信息都可通过J.克雷格文特尔研究所维持的项目网站（http：//www.jcvi.org/cms/research/projects/medicago-truncatula-database/overview/）免费查阅，该项目将由一个咨询委员会监测，该委员会由社区选出的国际苜蓿指导委员会成员组成。在教育方面，两个参与机构将在其实验室接待来访学生进行暑期实习。此外，还将举办年度讲习班，向豆类社区的研究生、博士后研究员和感兴趣的教员提供基因组注释和分析方面的教育。