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.

主要研究者：克洛德·德帕姆（宾夕法尼亚州立大学）联合PI：马洪（宾夕法尼亚州立大学），吉姆·利本斯-麦克（格鲁吉亚大学），帕梅拉·索迪斯（佛罗里达大学），道格拉斯索蒂斯（佛罗里达大学）高级人员：桑德拉克利夫顿（华盛顿大学），娜奥米·奥特曼（宾夕法尼亚州立大学）。开花植物的起源和早期多样化（被子植物）对地球的生物区系有着深远的影响，并提供了所有经济上重要的被子植物作物的原始遗传材料。单子叶植物和真双子叶植物被子植物的基因组、基因、调控过程和许多特定适应的进化，如果没有一个与基底被子植物基因组序列牢固相连的比较框架，就不能得到充分的解释。然而，对于基因组，或就此而言，对几乎现存的开花植物的大多数基因知之甚少，这些植物代表了我们与最早的被子植物的唯一幸存联系。有限的EST数据，从早期花发育的花基因组计划，提供了我们唯一的线索，基因组存在于祖先被子植物。这些数据表明，最早的开花植物有一个大的和分歧的基因组有助于开花过程，并可能经历了多倍体事件之前，现存的谱系多样化。 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，旨在提供对所有被子植物的比较框架的发展至关重要的资源：1）基础被子植物谱系和一种裸子植物的比较“深层转录组测序”-AAGP将尽可能全面地标记和测序五种遗传学关键的基础被子植物的转录组：Amborella，Nuphar，Persea，Liriodendron和Aristolochia。与苏铁泽米和其他现有裸子植物数据的可比EST数据集一起，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部分开花植物基因和基因家族的祖先状态提供强有力的证据。2)Amborella的BAC文库指纹图谱和物理图谱-将对Amborella的现有高质量BAC文库进行末端测序、指纹图谱和组装，以生成Amborella的物理图谱。 将选择40个克隆用于对这种植物遗传学上关键的被子植物基因组的小但科学上重要的部分进行概念验证测序。这张图将使我们有可能确定基因组规模的重复事件，而BAC末端序列将提供有关基因和其他序列在祖先被子植物的连锁模式的第一个信息。 3)生物信息学平台-现有的信息学结构将被扩展，使所有的数据都可以通过工具轻松访问，以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)推广-AAGP将把推广工作集中在两个领域：a）与历史上的黑人大学的教师和学生开展一项试点跨文化指导计划，重点是生物信息学技能和基因组分析，以及B）关于祖先被子植物的科学推广。公众参与了解祖先被子植物将鼓励通过两个公开呼吁公众投入Amborella BAC克隆测序。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，用于交互式检查每个研究物种的基因空间、序列、遗传学和表达信息，以及关于祖先被子植物的推论。