After the Sequencing: Curating the Medicago Truncatula Genome

PI：克里斯托弗·D·唐恩，J.克雷格·文特尔研究所，Inc.合作：大卫·C·施瓦茨，威斯康星大学的大卫·C·施瓦茨，紫花苜蓿的近亲，是豆科植物基因组学的卓越模式，在过去的五年里一直是一项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~280Mb的高质量DNA序列分布在该植物的8条染色体上，每条染色体上的序列块大小从几十万个碱基到500-1000万个碱基不等，每个常染臂上有10-30个缺口。根据表达序列标签的预计捕获率，基因组中常染色质、富含基因的部分将完成约80%。着丝粒中也将有~200Mb的未测序DNA，这是基因贫乏的，也不是测序的目标。该项目将整合、管理和加强我们对紫花苜蓿基因组的结构和注释的理解，并包括三个目标：1.创建基于序列的最好的元宝草基因组表示法。这将涉及构建光学图谱，这是一个物理支架，由完全独立于DNA测序过程的方法得出。该图谱将允许由测序中心产生的DNA序列(重叠群)的连续延伸以正确的顺序和方向放置，并且这些重叠群之间的间隙的大小以及基因缺失着丝粒区域的位置和大小将被确定。以最具成本效益的方式尽可能多地捕获和定位元胞杆菌基因组中剩余的包含基因的区域，从而提供接近于完整的基因内容清单。支持和维护IMGAG(International Medicago Genome Annotation Group)注释管道，该管道代表了整个Medicago(和豆类)社区的共识注释过程，并通过覆盖其他数据类型，包括表达数据(微阵列和下一代测序)、蛋白质组数据、转座子和快中子诱导的突变位置、与遗传资源的链接等，丰富了元宝菇基因组的注释。随着测序计划的终止，IMGAG联盟的成员(包括美国的JCVI小组)将没有多少资源用于继续注释。该项目将维护和更新紫花苜蓿基因组的序列内容和注释，并为未来几年的豆科研究人员提供关键的中央和稳定的资源。该项目还将建立一个社区注释门户，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自动的计算机生成的注释。该项目产生的所有信息将通过J.克雷格·文特尔研究所维护的项目网站免费获取，(http://www.jcvi.org/cms/research/projects/medicago-truncatula-database/overview/).The项目将由一个由社区选举的国际紫花苜蓿指导委员会成员组成的咨询委员会进行监测。在教育层面，这两所参与院校将在其实验室接待来访的学生进行暑期实习。此外，还将举办年度研讨会，为研究生、博士后研究员和豆科社区感兴趣的教师提供基因组注释和分析方面的教育。

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.