The Amborella Genome: A Reference for Plant Biology

PI：Claude W.宾夕法尼亚州立大学CoPI：维克托A。阿尔伯特（布法罗大学），W。布拉德巴尔巴祖克（佛罗里达大学-盖恩斯维尔），詹姆斯利本斯-麦克（格鲁吉亚大学-雅典），马洪（宾夕法尼亚州立大学），道格拉斯E。Soltis（佛罗里达大学-盖恩斯维尔）和Pamela S. Soltis（佛罗里达-盖恩斯维尔大学）帕尔默（印第安纳州州立大学），史蒂芬D. Rounsley（亚利桑那大学），Stephan C. Schuster（宾夕法尼亚州立大学）和Susan R.开花植物（被子植物）的起源和早期多样化对地球生物群产生了深远的影响，为大多数作物和经济上重要的植物提供了原始遗传物质。基因、基因组和重要性状的多样性，如果没有一个与基生被子植物基因组序列紧密相连的比较框架，就不能得到充分的解释。研究结果为被子植物基因组结构和基因含量的比较分析奠定了基础。在基础被子植物中，Amborella拥有最广泛的基因组资源，已经拥有高质量的基因组文库，物理图谱和大型表达基因（转录组）数据库。这些资源，沿着其关键的系统发育位置和中等的基因组大小（8.7亿个碱基对），使Amborella成为第一个被完全测序的基底被子植物的唯一选择。Amborella基因组计划将：1）完成Amborella的物理图谱; 2）使用“下一代”测序方法和成本效益高的策略生成Amborella基因组的高质量草图序列和组装，该策略已在水稻基因组上进行了测试，上级传统的测序方法;以及3）开发生物信息学工具和公共访问网站，以展示项目数据库的制作情况，并支持广大科学界进行比较分析和数据挖掘。Amborella基因组以及用于获得和分析基因组的策略将提供广泛影响植物生物学的独特科学资源，以及展示比较基因组学在生物科学中的实用性的绝佳机会。被子植物基因组的内容和组织的参考将有利于所有现有的被子植物基因组序列的分析和那些在未来获得的。 将为初中和高中教师举办比较基因组学讲习班，并将创建广泛传播项目成果和利用比较基因组学的教学模块。此外，该项目将扩大一个成功的跨文化科学指导计划，涉及每个参与大学的少数民族本科生，培训博士后科学家和研究生，并为市中心的高中生创造指导机会，帮助他们考虑植物科学的职业生涯。对博士后的具体指导活动将促进他们的专业发展。 项目网站（www.Amborella.org）将向公众提供所有数据、项目成果和长期储存库。所有序列数据将在其可用时存入NCBI，图像数据将存入Morphbank（http：//www.morphbank.net/）。

PI: Claude W. dePamphilis (Pennsylvania State University)CoPIs: Victor A. Albert (University at Buffalo), W. Brad Barbazuk (University of Florida - Gainesville), James Leebens-Mack (University of Georgia - Athens), Hong Ma (Pennsylvania State University), Douglas E. Soltis (University of Florida - Gainesville), and Pamela S. Soltis (University of Florida - Gainesville)Collaborators: Jeffrey D. Palmer (Indiana State University), Steven D. Rounsley (University of Arizona), Stephan C. Schuster (Pennsylvania State University), and Susan R. Wessler (University of Georgia - Athens) The origin and early diversification of flowering plants (angiosperms) had profound impacts on Earth's biota, providing the raw genetic material from which most crops and economically important plants were derived. The diversification of genes, genomes, and important traits cannot be adequately interpreted without a comparative framework firmly rooted with genome sequences from basal angiosperms. A genome sequence of Amborella trichopoda will provide a foundation for all comparative analyses of angiosperm gene content and genome structure. Among basal angiosperms, Amborella has the most extensive genomic resources, already possessing high-quality genomic libraries, a physical map, and a large expressed gene (transcriptome) database. These resources, along with its pivotal phylogenetic position and moderate genome size (870 million base pairs), make Amborella the singular choice for the first basal angiosperm to be fully sequenced. The Amborella genome project will: 1) complete the physical map of Amborella; 2) generate a high-quality draft sequence and assembly of the Amborella genome using "next generation" sequencing methods and a cost-effective strategy that has been tested on rice genomes and is superior to traditional sequencing methodologies; and 3) develop bioinformatic tools and public access websites to display the project database as it is produced, and support comparative analyses and data mining by the scientific community at large.Broader Impacts: The Amborella genome, and the strategies being used to obtain and analyze the genome, will provide a unique scientific resource broadly impacting plant biology as well as excellent opportunities to demonstrate the utility of comparative genomics across the biological sciences. A reference for angiosperm genome content and organization will benefit the analysis of all currently available angiosperm genome sequences and those that are obtained in the future. Comparative genomics workshops for middle and high school teachers will be held and teaching modules for broad dissemination of project outcomes and the utility of comparative genomics will be created. In addition, the project will expand a successful cross-cultural scientific mentoring program involving minority undergraduate students at each of the participating universities, train postdoctoral scientists and graduate students, and create mentoring opportunities for inner-city high school students to help them consider careers in the plant sciences. Specific mentoring activities for the post-docs will enhance their professional development. The project website (www.Amborella.org) will provide public access to all data, project results, and long-term repositories. All sequence data will be deposited to NCBI as they become available and image data will be deposited at Morphbank (http://www.morphbank.net/).