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: Rod a . Wing（亚利桑那大学）合作PI: Scott a . Jackson（普渡大学），Steven D. Rounsley（亚利桑那大学），Lincoln D. Stein（冷泉港实验室）比较基因组学是了解基因和基因组如何功能和进化的强大工具，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了解物种形成、多倍体化、驯化和基因调控至关重要。目前，对高等真核生物最先进的属级比较系统是果蝇比较基因组测序项目（Drosophila comparative genome sequencing project）和Oryza map alignment project (OMAP)，分别对12个野生果蝇基因组进行测序、组装并与参考果蝇基因组进行比对。OMAP项目绘制了12个野生水稻基因组的物理图谱，并与参考水稻水稻基因组进行比对。该项目的长期目标是创建一个具有广泛用途的免费可用的比较序列资源，可以询问基因组生物学，进化和驯化属的基本问题。为了实现这一目标，水稻3号染色体短臂在3个二倍体基因组（AA、BB和CC）及其异源四倍体后代（BBCC）上的BAC平铺路径将被测序并严格注释。本项目生成的序列将在以下方面对科学界具有广泛的实用价值：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元件的比较信息（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和其他野生稻所特有的基因和转座因子。对于栽培物种，这些独特的基因可能在驯化中发挥重要作用，并将优先进行功能分析。对于野生稻而言，这些独特的基因可能对其生存和适应特定的环境起着重要的作用。3)该序列还将为3号染色体短臂发生重排（如插入、缺失、倒位和易位）的区域提供前所未有的数据集。通过将这些重排与基因图谱相结合，我们将能够对重排、扩展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的作用提出基本问题。除了这项提议在科学上的广泛影响外，还将针对代表性不足的大学生和教师提供暑期基因组学拓展培训计划，将课堂上获得的知识应用和扩展到实践经验中。学生将有机会看到生物学的职业生涯，并将被鼓励继续他们的教育，通过硕士和博士水平。实习生将在为期八周的暑期课程中全职参与PI实验室。每个学生将与一名导师配对，导师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。获取项目成果项目成果将以同行评议期刊和Gramene公共谷物数据库（http://www.gramene.org）的出版物形式提供。所有序列和跟踪文件数据将存储在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/).