The Ancestral Angiosperm Genome Project

祖先被子植物基因组计划

• 批准号: 0638595
• 负责人: Claude dePamphilis
• 金额: $ 308.77万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-01-01 至 2011-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0638595&HistoricalAwards=false
• 关键词: Ancestral; Angiosperm; Genome; Project

PI: Claude dePamphilis (Penn State University)Co-PIs: Hong Ma (Penn State University), Jim Leebens-Mack (University of Georgia), Pamela Soltis (University of Florida), Douglas Soltis (University of Florida)Senior Personnel: Sandra Clifton (Washington University), Naomi Altman (Penn State University).The origin and early diversification of flowering plants (angiosperms) had profound impacts on Earth's biota and provided the raw genetic material from which all economically important angiosperm crop plants were derived. The evolution of genomes, genes, regulatory processes, and numerous specific adaptations in monocot and eudicot angiosperms cannot be adequately interpreted without a comparative framework firmly rooted with genome sequences from basal angiosperms. However, little is known about the genomes or, for that matter, most genes of the basalmost extant flowering plants, which represent our sole surviving links to the earliest angiosperms. Limited EST data, generated from early flower development in the Floral Genome Project, provide our only clues to the gene set present in the Ancestral Angiosperm. These data suggest that the earliest flowering plants had a large and diverge set of genes contributing to the flowering process, and may have undergone a polyploid event just prior to diversification of extant lineages. The Ancestral Angiosperm Genome Project (AAGP) is built around three primary experimental and analytical objectives, designed to provide resources that are essential to the development of a comparative framework to all angiosperms: 1) Comparative "deep transcriptome sequencing" of basal angiosperm lineages and one gymnosperm - The AAGP will tag and sequence, as fully as possible, the transcriptomes of five phylogenetically critical, basal angiosperms: Amborella, Nuphar, Persea, Liriodendron, and Aristolochia. Together with a comparable EST dataset for the cycad Zamia and other existing gymnosperm data, these species will surround the ancestral angiosperm node and will provide strong evidence for inferring the ancestral state of the angiosperm transcriptome and a large majority of flowering plant genes and gene families. 2) BAC library fingerprinting and physical mapping of Amborella - An existing high quality BAC library of Amborella will be end sequenced, fingerprinted, and assembled to generate a physical map of Amborella. 40 clones will be selected for proof-of-concept sequencing of small but scientifically important portions of the genome of this phylogenetically pivotal angiosperm. This map should make it possible to identify genome-scale duplication event, while the BAC end sequence will provide the first information about the linkage patterns of genes and other sequences in the ancestral angiosperm. 3) Bioinformatic platform - Existing informatic structures will be expanded to make all of the data readily accessible with tools to help researchers access and study in a comparative genomic framework any plant gene, gene family, or otherwise defined gene set. 4) Outreach - The AAGP will focus outreach efforts in two areas: a) a pilot crosscultural mentoring program with faculty and students at historically black universities, with a focus on bioinformatic skills and genomic analysis, and b) scientific outreach on the Ancestral Angiosperm. Public involvement in understanding the Ancestral Angiosperm will be encouraged through two open calls for public input on Amborella BAC clones to be sequenced. Access to project outcomesAll sequence data will be deposited immediately in GenBank (http://www.ncbi.nlm.nih.gov/), with www.floralgenome.org providing comprehensive database access and analytical tools for the interactive examination of the gene space, sequences, phylogeny, and expression information for each of the study species and inferences about the Ancestral Angiosperm.

PI：Claude de Pamphilis（宾夕法尼亚州立大学）Co-PI：Hong Ma（宾夕法尼亚州立大学）、Jim Leebens-Mack（佐治亚大学）、Pamela Soltis（佛罗里达大学）、Douglas Soltis（佛罗里达大学）高级人员：Sandra Clifton（华盛顿大学）、Naomi Altman（宾夕法尼亚州立大学）。开花植物（被子植物）的起源和早期多样化产生了深远的影响地球生物群，并提供了所有经济上重要的被子植物作物的原始遗传物质。如果没有牢固植根于基础被子植物基因组序列的比较框架，就无法充分解释单子叶植物和真双子叶被子植物的基因组、基因、调控过程和许多特定适应的进化。然而，人们对基因组知之甚少，或者说，对现存最基础的开花植物的大多数基因知之甚少，它们代表了我们与最早的被子植物唯一幸存的联系。花卉基因组计划中早期花卉发育产生的有限 EST 数据为我们提供了有关祖先被子植物基因组的唯一线索。这些数据表明，最早的开花植物具有大量且不同的基因，有助于开花过程，并且可能在现存谱系多样化之前经历了多倍体事件。 祖先被子植物基因组计划 (AAGP) 围绕三个主要实验和分析目标建立，旨在提供开发所有被子植物比较框架所必需的资源：1) 基础被子植物谱系的比较“深度转录组测序”和一个裸子植物 - AAGP 将尽可能完整地对五种系统发育关键的基础被子植物的转录组进行标记和测序： Amborella、Nuphar、Persea、Liriodendron 和 Aristolochia。与苏铁 Zamia 的可比 EST 数据集和其他现有裸子植物数据一起，这些物种将围绕祖先被子植物节点，并将为推断被子植物转录组和大多数开花植物基因和基因家族的祖先状态提供有力的证据。 2) Amborella 的 BAC 文库指纹识别和物理图谱 - 对现有的高质量 Amborella BAC 文库进行末端测序、指纹识别和组装，以生成 Amborella 的物理图谱。 将选择 40 个克隆，对这一系统发育关键的被子植物基因组中虽小但具有科学重要性的部分进行概念验证测序。该图谱应该能够识别基因组规模的重复事件，而 BAC 末端序列将提供有关祖先被子植物中基因和其他序列的连锁模式的第一个信息。 3) 生物信息平台——现有的信息结构将得到扩展，以便通过工具轻松访问所有数据，帮助研究人员在比较基因组框架中访问和研究任何植物基因、基因家族或其他定义的基因集。 4) 外展——AAGP 将把外展工作重点放在两个领域：a) 与历史悠久的黑人大学的教职员工和学生一起开展跨文化指导试点项目，重点关注生物信息学技能和基因组分析；b) 关于祖先被子植物的科学外展。将通过两次公开呼吁公众对 Amborella BAC 克隆进行测序提供意见，鼓励公众参与了解祖先被子植物。获取项目成果所有序列数据将立即存入 GenBank (http://www.ncbi.nlm.nih.gov/)，www.floralgenome.org 提供全面的数据库访问和分析工具，用于基因空间的交互式检查每个研究物种的序列、系统发育和表达信息以及有关祖先被子植物的推论。