U.S. Contribution to the International Solanaceae Genome Effort

美国对国际茄科基因组工作的贡献

• 批准号: 0605659
• 负责人: James Giovannoni
• 金额: --
• 依托单位: Boyce Thompson Institute Plant Research
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-12-01 至 2009-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0605659&HistoricalAwards=false
• 关键词: U.S.; Contribution; International; Solanaceae; Genome

PI James Giovannoni (Boyce Thompson Inst. for Plant Research)Co-PIs Lukas Mueller (Cornell Univ.), Stephen Stack (Colorado State Univ.), Steven Tanksley (Cornell Univ.), Joyce Van Eck (Boyce Thompson Inst. for Plant Research)Key Collaborators Chuanyou Li, Ying Wang (Chinese Acad. Sci., China), Mondher Bouzayen, Farid Regad (INRA, France), Akhilesh Tyagi, Arun Sharma (Univ. of Delhi South Campus, India), Daniel Zamir (Hebrew Univ., Israel), Giovanni Giuliano (ENEA, Italy), Satoshi Tabata, Daisuke Shibata (Kazusa DNA Res. Inst., Japan), Doil Choi (KRIBB, Korea), Miguel Botella (Univ. Malaga,Spain), Antonio Granell (IBMCP, Spain), Pim Lindhout, Hans de Jong (Wageningen Univ., The Netherlands), Willem Stiekema (Centre for BioSystems Genomics, The Netherlands), Gerard Bishop (Univ. Wales, U.K.); Graham Seymour (Hort. Res. Inst., U.K.)Scientific objectives and approaches: In the tomato genome, euchromatin occurs in long contiguous stretches at the end of each chromosome. Euchromatin accounts for only 25% of the DNA, yet contains more than 90% of the estimated 38,000 genes. As part of an international consortium to sequence the euchromatin of all twelve tomato chromosomes, we will provide clone and informatic resources towards an international effort to sequence a minimal tiling path of BAC clones through this gene-rich DNA. The project will: 1) Coordinate the international sequencing effort by supplying verified BAC clones for sequencing and performing the necessary genetic and physical mapping required to guide sequencing through the euchromatin. 2) Continue to serve the international project as a central repository and web interface for all sequence and annotation data. 3) Contribute to the structural and functional annotation for the genomic sequence with the international collaborators. 4) Continue to develop integrated bioinformatics for genomic research in the Solanaceae and related taxa through the SOL Genome Network database. This will include computationally mapping ESTs and other gene sequences from related species (e.g. potato, eggplant, pepper, coffee, etc.) onto the tomato reference sequence in order to generate predictive sequence maps for those species.Broader impacts of project: Sequencing the tomato genome is the cornerstone of a larger international effort: "The International Solanaceae Genome Initiative" or "SOL Initiative". The tomato reference sequence will provide gene content and order, which is well documented to be similar to other Solanaceae genomes, thus making the phenotypic and evolutionary diversity in this family accessible for exploration at the sequence level. The tomato genome is connected to the other important members of the family by detailed comparative genetic maps and the level of microsynteny is known to be well conserved (gene content and order). Because the Solanaceae represents a distinct and divergent clade of flowering plants, distant from Arabidopsis, Medicago, soybean, maize and rice, the tomato sequence will also provide a rich resource for investigating the forces of gene and genome evolution over long periods of evolutionary time.We will continue our Bioinformatics Summer Intern Program, in addition to offering research/computational biology opportunities to students during the academic year. Assignment of projects to students will serve two purposes by providing training opportunities while simultaneously advancing the goals of our proposed research. We are committed to the recruitment of students from underrepresented groups to both provide novel opportunities and experiences and to foster confidence in pursuit of broader career goals by working in a diverse group. Providing such opportunities could impact the diversity of students who go on to pursue this area of research or scientific careers in general.Access to project outcomesAll data will be accessible via the Solanaceous Genomes Network (SGN: http://www.sgn.cornell.edu/).

Pi James Giovannoni(Boyce Thompson Inst.植物研究)联合PIS Lukas Mueller(康奈尔大学)，Stephen Stack(科罗拉多州立大学)，Steven Tanksley(康奈尔大学)，Joyce Van Eck(Boyce Thompson Inst.植物研究)主要合作者李传友、王颖(中国植物研究)。科学，中国)，Mondher Bouzayen，Farid Regad(法国，INRA)，AkHilesh Tyagi，Arun Sharma(大学)印度德里南校区)，Daniel Zamir(希伯来大学，以色列)，Giovanni Giuliano(ENEA，意大利)，Satoshi Tabata，Daisuke Shibata(Kazusa DNA Res.Inst，日本)，doil Choi(KRIBB，韩国)，Miguel Boella(大学Pim Lindhout、Hans de Jong(荷兰瓦赫宁根大学)、Willem Stiekema(荷兰生物系统基因组学中心)、Gerard Bishop(荷兰大学)。英国威尔士)；格雷厄姆·西摩(Hort.科学目标和方法：在番茄基因组中，常染色质出现在每条染色体末端的长而连续的伸展上。常染色质只占DNA的25%，但却包含了约38000个基因中的90%以上。作为对所有12条番茄染色体常染色质测序的国际联盟的一部分，我们将提供克隆和信息资源，用于通过这种富含基因的DNA对BAC克隆的最小平铺路径进行排序的国际努力。该项目将：1)协调国际测序工作，提供用于测序的经验证的BAC克隆，并进行必要的基因和物理图谱，以指导通过常染色质的测序。2)继续将国际项目作为所有序列和注释数据的中央储存库和网络接口。3)与国际合作者一起为基因组序列的结构和功能注释做出贡献。4)通过SOL基因组网络数据库，继续为茄科和相关类群的基因组研究开发综合生物信息学。这将包括对来自相关物种(例如土豆、茄子、辣椒、咖啡等)的EST和其他基因序列进行计算作图。项目的广泛影响：对番茄基因组测序是一项更大的国际努力的基石：“国际茄科基因组倡议”或“SOL倡议”。番茄参考序列将提供与茄科其他基因组相似的基因内容和序列，从而使该家族的表型和进化多样性能够在序列水平上进行探索。番茄基因组通过详细的比较遗传图谱与该家族的其他重要成员相连，微同步水平被认为是非常保守的(基因含量和顺序)。由于茄科代表着一个独特而不同的开花植物分支，远离拟南芥、紫花苜蓿、大豆、玉米和水稻，番茄序列也将为研究长期进化过程中基因和基因组进化的力量提供丰富的资源。我们将继续我们的生物信息学暑期实习生计划，除了在学年为学生提供研究/计算生物学的机会。分配给学生的项目将有两个目的，即提供培训机会，同时推进我们提议的研究目标。我们致力于从代表性不足的群体中招收学生，以提供新的机会和经验，并通过在不同的群体中工作来培养追求更广泛职业目标的信心。提供这样的机会可能会影响继续从事这一研究领域或一般科学职业的学生的多样性。获得项目成果所有数据将通过茄科基因组网络(sgn：http://www.sgn.cornell.edu/).)获得