The Amborella Genome: A Reference for Plant Biology

合作者：维克多·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-盖恩斯维尔分校)、詹姆斯·利本斯-马克(佐治亚大学-雅典分校)、洪马(宾夕法尼亚州立大学)、道格拉斯·E·索尔蒂斯(佛罗里达大学-盖恩斯维尔分校)和帕梅拉·索尔蒂斯(佛罗里达大学-盖恩斯维尔分校)合作者：杰弗里·D·帕尔默(印第安纳州立大学)、史蒂文·D·罗恩斯利(亚利桑那大学)、斯蒂芬·C·舒斯特(宾夕法尼亚州立大学)、和苏珊·R·韦斯勒(佐治亚大学雅典分校)开花植物(被子植物)的起源和早期多样化对地球的生物群产生了深远的影响，为大多数农作物和重要的经济作物提供了原始的遗传物质。如果没有一个牢固地植根于基生被子植物基因组序列的比较框架，就不能充分解释基因、基因组和重要性状的多样性。毛足类Amborella的基因组序列将为被子植物基因含量和基因组结构的所有比较分析提供基础。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、物理图谱和庞大的表达基因(转录组)数据库。这些资源，加上其关键的系统发育地位和适中的基因组大小(8.7亿碱基对)，使Amborella成为第一个完全测序的基础被子植物的唯一选择。安博雷拉基因组计划将：1)完成安博雷拉的物理图谱；2)使用“下一代”测序方法和成本效益策略产生高质量的安博雷拉基因组草图和组装，该策略已经在水稻基因组上进行了测试，并优于传统的测序方法；3)开发生物信息学工具和公共访问网站，以显示产生的项目数据库，并支持科学界的比较分析和数据挖掘。广泛影响：Amborella基因组以及用于获取和分析基因组的策略，将提供一个独特的科学资源，对植物生物学产生广泛影响，并提供极好的机会，展示比较基因组学在生物科学中的效用。被子植物基因组内容和组织的参考将有助于分析目前所有可用的被子植物基因组序列和未来获得的那些序列。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比较基因组学实用的教学单元。此外，该项目将扩大一个成功的跨文化科学指导计划，让每所参与大学的少数族裔本科生参与，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，帮助他们考虑在植物科学领域就业。针对博士后的具体辅导活动将促进他们的专业发展。项目网站(www.Amborella.org)将提供对所有数据、项目成果和长期储存库的公开访问。所有序列数据将在可用时存储到NCBI，图像数据将存储在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/).