U.S. Contribution to the International Solanaceae Genome Effort

PI James Giovannoni（博伊斯汤普森植物研究所）Co-PI Lukas Mueller（康奈尔大学），斯蒂芬·斯塔克（科罗拉多州立大学），Steven Tanksley（康奈尔大学），Joyce货车Eck（博伊斯汤普森植物研究所）主要合作者李传友，王颖（中国科学院院士）科学，中国），Mondher Bouzayen，Farid Regad（INRA，法国），Akhilesh Tyagi，Arun Sharma（德里大学南校区，印度），丹尼尔扎米尔（希伯来大学，以色列）、Giovanni Giuliano（ENEA，意大利）、Satoshi Tabata、Daisuke柴田（Kazusa DNA Res. Inst.，日本）、Dolil Choi（韩国KRIBB）、Miguel Botella（西班牙马拉加大学）、Antonio Granell（西班牙IBMCP）、Pim Lindhout、Hans de Jong（瓦赫宁根大学，荷兰）、Willem Stiekema（荷兰生物系统基因组学中心）、Gerard Bishop（英国威尔士大学）; Graham Seymour（Hort. Res. Inst.，（联合王国）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连续延伸中。常染色质仅占DNA的25%，但包含估计38，000个基因中的90%以上。作为对所有12条番茄染色体的常染色质进行测序的国际联盟的一部分，我们将提供克隆和信息资源，以通过这种基因丰富的DNA对BAC克隆的最小平铺路径进行测序。该项目将：1）通过提供用于测序的经验证的BAC克隆并进行指导通过常染色质测序所需的必要遗传和物理作图来协调国际测序工作。2)继续作为所有序列和注释数据的中央储存库和网络接口为国际项目服务。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)继续通过SOL基因组网络数据库为茄科和相关分类群的基因组研究开发综合生物信息学。这将包括计算绘制EST和相关物种（如马铃薯、茄子、辣椒、咖啡等）的其他基因序列。项目的更广泛影响：番茄基因组测序是一项更大的国际努力的基石：“国际茄科基因组计划”或“SOL计划”。番茄参考序列将提供基因内容和顺序，这是有据可查的是类似于其他茄科基因组，从而使该家庭的表型和进化多样性可用于在序列水平上的探索。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，并且已知微共线性水平是很保守的（基因内容和顺序）。由于茄科代表了一个独特的和不同的开花植物的分支，远离拟南芥，苜蓿，大豆，玉米和水稻，番茄序列也将提供一个丰富的资源，研究的力量基因和基因组进化在很长一段时间的进化时间。我们将继续我们的生物信息学暑期实习生计划，除了提供研究/计算生物学的机会，学生在学年。项目分配给学生将通过提供培训机会，同时推进我们提出的研究目标，达到两个目的。我们致力于从代表性不足的群体中招募学生，以提供新颖的机会和经验，并通过在多元化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学生的多样性，他们将继续从事这一领域的研究或科学事业。

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/).