The Ancestral Angiosperm Genome Project

PI: Claude dePamphilis（宾夕法尼亚州立大学）合作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对地球生物群产生了深远的影响，并为所有具有重要经济意义的被子植物作物提供了原始遗传物质。如果没有一个牢固植根于基生被子植物基因组序列的比较框架，就无法充分解释单子叶被子植物和双子叶被子植物的基因组、基因、调控过程和许多特定适应性的进化。然而，我们对这些几乎现存的开花植物的基因组知之甚少，或者说，对它们的大部分基因知之甚少，而这些开花植物是我们与最早的被子植物唯一存活的联系。有限的EST数据来自花基因组计划中的早期花发育，为我们提供了祖先被子植物中存在的基因集的唯一线索。这些数据表明，最早的开花植物拥有大量不同的基因，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）是围绕三个主要的实验和分析目标建立的，旨在为所有被子植物的比较框架的发展提供必要的资源：1)基生被子植物谱系和裸子植物的比较“深度转录组测序”- AAGP将尽可能全面地标记和测序5种系统发育关键的基生被子植物的转录组；安柏属，努法属，波斯属，鹅掌楸属，马兜铃属。与苏铁Zamia和其他现有裸子植物数据的可比EST数据集一起，这些物种将围绕被子植物祖先节点，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强有力的证据。2) Amborella的BAC文库指纹图谱和物理图谱——将对现有的高质量Amborella 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个克隆对这种系统发育关键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。该图谱将使鉴定基因组级复制事件成为可能，而BAC端序列将提供有关祖先被子植物基因连锁模式和其他序列的第一手信息。3)生物信息学平台——现有的信息结构将被扩展，使所有的数据都可以通过工具方便地访问，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)外联——AAGP将把外联工作重点放在两个方面：a)与传统黑人大学的教职员工和学生开展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；b)关于祖先被子植物的科学外联。通过两次公开征集公众对Amborella BAC克隆测序的意见，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，用于对每个研究物种的基因空间、序列、系统发育和表达信息进行交互检查，并推断出祖先被子植物。

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.