After the Sequencing: Curating the Medicago Truncatula Genome

联合负责人：David C. Schwartz，威斯康星大学的medicago truncatula，苜蓿的近亲，是豆科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，将有大约280 Mb的高质量DNA序列分布在植物的8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到1000万个碱基不等，每个常染色臂上有10-30个间隙。根据所表达序列标签的预计捕获率，基因组的常染色、基因丰富的部分将完成80%左右。在着丝粒中也会有大约200mb的未测序DNA，这些DNA是基因贫乏的，不是测序的目标。该项目将整合、管理和增强我们对Medicago基因组结构和注释的理解，主要包括三个目标：1。创造最好的基于序列的M. truncatula基因组代表。这将涉及光学图谱的构建，这是一个完全独立于DNA测序过程的物理支架。该图谱将允许由测序中心产生的DNA序列（contigs）的连续延伸以正确的顺序和方向排列，并确定这些contigs之间的间隙大小以及基因贫乏的着丝粒区域的位置和大小。以最具成本效益的方式尽可能多地捕获和定位M. truncatula基因组中剩余的含基因区域，从而提供其基因含量的接近完整的清单。支持和维护IMGAG （International Medicago Genome Annotation Group）注释管道，该管道代表了整个Medicago（和豆科植物）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（包括微阵列和下一代测序）、蛋白质组学数据、转座子和快中子诱导突变的位置、遗传资源链接等，丰富了M. truncatula基因组的注释。随着测序项目的终止，IMGAG联盟成员（包括美国的JCVI集团）将没有多少资源用于继续注释。该项目将维护和更新Medicago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重要的中心和稳定的资源。该项目还将建立一个社区注释门户，允许研究人员根据自己的知识和经验，用更精细的结构和功能细节来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. Craig Venter研究所维护的项目网站（http://www.jcvi.org/cms/research/projects/medicago-truncatula-database/overview/）.The)免费获取。该项目将由社区选举的国际医疗指导委员会成员组成的咨询委员会监督。在教育层面，两家参与机构将在其实验室接待访问学生进行暑期实习。此外，每年还将举办研讨会，为研究生、博士后和对豆类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.