Sequencing of Chromosome 3 Short Arms From the AA, BB, CC, BBCC Genomes of Wild Relatives of Rice for Comparative Functional and Evolutionary Genomics

PI：棒A。Wing（亚利桑那大学）Co-PI：Scott A.杰克逊（普渡大学），史蒂芬D. Rounsley（亚利桑那大学），林肯D. Stein（冷泉港实验室）比较基因组学是了解基因和基因组功能和进化的有力工具，但对属内物种基因组的比较研究有限。这种比较对于更深入地理解物种形成、多倍化、驯化和基因调控至关重要。可用于高等真核生物的两个最先进的属级比较系统是果蝇比较基因组测序计划，其中12个野生果蝇基因组被测序、组装并与参考D.和Oryza map alignment project（OMAP），这两个图谱是对12个野生稻基因组的物理图谱，并与参考野生稻进行了比对。该项目的长期目标是创建具有广泛实用性的可免费获得的比较序列资源，其可以被询问以询问稻属中的基因组生物学、进化和驯化中的基本问题。为了实现这一目标，将对水稻3号染色体短臂在三个二倍体基因组（AA、BB和CC）及其异源四倍体后代（BBCC）中的BAC平铺路径进行测序和严格注释。该项目产生的序列将在以下方面对科学界具有广泛的实用性：1）该序列将提供AA、BB、CC、BBCC基因组之间共有的所有基因和转座因子的比较信息（例如等位基因多样性，保守的非编码序列）。该序列将允许鉴定栽培稻以及其他野生物种所特有的基因和转座因子。对于栽培种，这些独特的基因可能在驯化过程中发挥重要作用，并将优先进行功能分析。就野生稻种质而言，这些独特的基因可能在它们起源的特定环境中的生存和适应中起重要作用。3）该序列还将在经历重排（例如插入、缺失、倒位和易位）的3号染色体短臂区域中提供前所未有的数据集。通过将这些重排与遗传图谱相结合，我们将能够提出关于重排、扩增和收缩在染色体物种形成、基因组大小维持和新基因进化中所起作用的基本问题。除了这一提议的更广泛的科学影响外，夏季基因组学外展培训计划将提供针对下-代表大学生和教职员工将课堂上获得的知识应用于实践经验。学生将有机会查看生物学职业生涯，并将被鼓励通过MS继续他们的教育。和博士程度.实习生将在为期八周的夏季课程中全职参加PI实验室。每个学生将与一位导师配对，他将帮助开发一个与实习生的特定兴趣和专业领域相一致的研究项目。项目成果将以同行评审期刊和Gramene公共谷物数据库（http：//www.example.com）出版物的形式提供。www.gramene.org 所有序列和跟踪文件数据将保存在Genbank（http：//www.ncbi.nlm.nih.gov/）中。

PI: Rod A. Wing (University of Arizona)Co-PIs: Scott A. Jackson (Purdue University), Steven D. Rounsley (University of Arizona), Lincoln D. Stein (Cold Spring Harbor Laboratory)Comparative genomics is a powerful tool to understand how genes and genomes function and evolve yet limited studies have been done comparing the genomes of species within a genus. Such comparisons are critical for a deeper understanding of speciation, polyploidization, domestication and gene regulation. The two most advanced genus level comparative systems available for higher eukaryotes are the Drosophila comparative genome sequencing project where 12 wild Drosophila genomes are being sequenced, assembled and compared to the reference D. melanogaster genome, and the Oryza map alignment project (OMAP) were physical maps of 12 wild rice genomes have been made and aligned to the reference O. sativa genome.The long term goal of this project is to create a freely available comparative sequence resource with broad utility that can be interrogated to ask fundamental questions in genome biology, evolution and domestication in the genus Oryza. To accomplish this goal, BAC tiling paths of the short arm of rice chromosome 3 across three diploid genomes (AA, BB and CC) and their allotetraploid progeny (BBCC) will be sequenced and rigorously annotated. The sequence generated from this project will have broad utility to the scientific community in the following ways: 1) The sequence will provide comparative information on all genes and transposable elements that are common between the AA, BB, CC, BBCC genomes (e.g. allelic diversity, conserved non-coding sequences).2) The sequence will permit the identification of genes and transposable elements that are unique to cultivated rice as well as to the other wild species. For cultivated species, the unique genes may play important roles in domestication and would be prioritized for functional analysis. With respect to the wild rice accessions, the unique genes may play important roles for survival and adaptation to particular environments where they originated.3) The sequence will also provide an unprecedented data set in regions of the short arm of chromosome 3 that have undergone rearrangements (e.g. insertions, deletions, inversions and translocations). By integrating these rearrangements with genetic maps we will be able ask fundamental questions on the role that rearrangements, expansions and contractions play in chromosome speciation, genome size maintenance and the evolution of new genes.In addition to the scientific broader impacts of this proposal, a summer genomics outreach training program will be offered targeting under-represented college students and faculty to apply and extend knowledge gained in the classroom to practical experience. Students will have the opportunity to view careers in biology and will be encouraged to continue their education through the M.S. and Ph.D. levels. Interns will participate full-time in a PI lab during eight-week summer sessions. Each student will be paired with a mentor who will help develop a research project that is in alignment with the intern's particular area of interest and expertise.Access to project outcomesProject outcomes will be available in the form of publications in peer-reviewed journals and the Gramene public cereal database (http://www.gramene.org). All sequence and trace file data will deposited in Genbank (http://www.ncbi.nlm.nih.gov/).