Sequencing the Aegilops tauschii Genome

PI：Jan Dvorak（加州大学戴维斯分校）CoPI：Ming-Cheng Luo（加州大学戴维斯分校），Katrien M. Devos（雅典格鲁吉亚大学），Steven Salzberg（约翰霍普金斯大学）和Yong Q。Gu和Olin D.安德森（USDA-ARS，奥尔巴尼/加州大学戴维斯分校）合作者：汉斯-乔治·穆勒（加州大学戴维斯分校），杰弗里·L. Bennetzen（雅典格鲁吉亚大学）、Zhiyong Liu（北京中国农业大学）、Philippe Leroy（法国INRA/IBP）、Eric里昂和Carol Soderlund（图森亚利桑那大学）、Zhengqiang Ma（中国南京农业大学）、Long Mao（中国农业科学院）、Klaus F.X. Mayer（Helmholtz Center，慕尼黑，德国），Richard W. McCombie（冷泉港实验室）、孙启新（西北农林科技大学）、托马斯威克（瑞士苏黎世大学）和弗兰克M.&你（加拿大农业和农业食品部，温尼伯）面包小麦是全球粮食供应的三大支柱之一。尽管小麦具有特殊的重要性，但主要由于其杂交起源（多倍体）及其基因组的巨大尺寸，小麦基因组的高质量草图序列不可用。为了协助国际面包小麦基因组测序工作，将制作面包小麦三大祖先之一的节节麦基因组的高质量草图。Ae的巨大尺寸和巨大复杂性。tauschii基因组需要采用有序克隆测序策略来产生高质量的基因组序列草图。这一策略将涉及对约50，000个含有Ae大片段的细菌人工染色体（BAC）克隆进行测序。已经被排序为代表Ae中核苷酸的连续序列的节节DNA。tauschii染色体DNA将用下一代DNA测序平台对1000个BAC克隆进行测序，并组装成长的连续序列。组装序列的正确性将通过一种新的光学纳米技术进行验证。组装序列中的基因和转座因子将被注释。通过这种方式，所有的基因和转座因子的序列，位置和方向的Ae。将确定节节麦基因组。最直接的影响是Ae。该项目所产生的tauschii基因组序列将用于预测小麦及其近缘种基因的位置，从而加速小麦及其近缘种基因组测序的进展，并有助于通过传统育种方法和生物技术发现和操纵这些物种的基因。的Ae。tauschii基因组序列将作为分析小麦起源以来小麦基因组发生的基因组变化的参考，为理解禾本科植物基因组结构和进化提供重要的基础性贡献。将基因组序列草案中预测的36，000多个基因与生物功能联系起来将是一项艰巨的任务。因此，该项目将吸引对分析Ae基因感兴趣的大型研究团体。以社区为基础的tauschii基因手工注释和图形结果汇编项目数据库。为了最大限度地提高小麦育种者和其他利益相关者对项目资源的认识，将在小麦育种者参加的专业会议上定期介绍/举办这些资源的研讨会。该项目还将为植物基因组学、生物信息学、DNA测序和序列组装、验证和分析方面的学生和博士后提供优秀的跨学科培训。BAC重叠群的验证序列和解析为单个BAC克隆的序列将每月存入项目网站（待开发）。所有序列都将保存在NCBI长期储存库中，并纳入Gramene、GrainGenes和MIPS比较数据库。从9个Ae. tauschii AL8/78和跨重叠群的最小平铺路径（MTP）是公开可得的，并通过www.example.com分发。

PI: Jan Dvorak (University of California, Davis) CoPIs: Ming-Cheng Luo (University of California, Davis), Katrien M. Devos (University of Georgia, Athens), Steven Salzberg (John Hopkins University) and Yong Q. Gu and Olin D. Anderson (USDA-ARS, Albany/University of California, Davis) Collaborators: Hans-Georg Müller (University of California, Davis), Jeffrey L. Bennetzen (University of Georgia, Athens), Zhiyong Liu (Chinese Agricultural University, Beijing), Philippe Leroy (INRA/IBP, France), Eric Lyons and Carol Soderlund (University of Arizona, Tucson), Zhengqiang Ma (Nanjing Agricultural University, China), Long Mao (Chinese Academy of Agricultural Sciences), Klaus F.X. Mayer (Helmholtz Center, Munich, Germany), Richard W. McCombie (Cold Spring Harbor Laboratory), Qixin Sun (Northwest A&F University, China), Thomas Wicker (University of Zurich, Switzerland) and Frank M. You (Agriculture and Agri-Food Canada, Winnipeg) Bread wheat is one of three pillars on which the global food supply rests. Despite wheat's exceptional importance, a high quality draft sequence of the wheat genome is not available due primarily to its hybrid origin (polyploidy) and the enormous size of its genome. To assist the international bread wheat genome sequencing effort, a high quality draft of the genome of Aegilops tauschii, one of the three progenitors of bread wheat, will be produced. The large size and great complexity of the Ae. tauschii genome necessitate adopting the ordered-clone sequencing strategy for generating a high quality genome sequence draft. This strategy will involve the sequencing of about 50,000 bacterial artificial chromosome (BAC) clones harboring large fragments of Ae. tauschii DNA that have been ordered to represent the contiguous sequence of nucleotides in Ae. tauschii chromosomal DNA. Pools of BAC clones will be sequenced with a next generation DNA sequencing platform and assembled into long contiguous sequences. The correctness of the assembled sequences will be validated with a novel optical nanotechnique. Genes and transposable elements in the assembled sequences will be annotated. In this way, the sequence, location, and orientation of all genes and transposable elements in the Ae. tauschii genome will be determined. The most immediate impact of the Ae. tauschii genome sequence produced by this project will be in predicting the location of genes in wheat and its relatives, thus accelerating progress in genome sequencing of wheat and its relatives and facilitating gene discovery and manipulation in these species through traditional breeding methods and biotechnology. The Ae. tauschii genome sequence will serve as a reference in analyses of genomic changes that have taken place in the wheat genome since wheat's origin, providing significant and fundamental contributions to the understanding of grass genome structure and evolution. Association of the more than 36,000 genes predicted within the draft genome sequence with biological functions will be a daunting task. For this reason, the project will engage the large research community interested in analyzing genes of Ae. tauschii in community-based manual gene annotation and graphical compilation of the results in the project database. To maximize the awareness about the project resources among the wheat breeders and other stakeholders, regular presentations/workshops of these resources will be made at professional meetings attended by wheat breeders. The project will also provide excellent interdisciplinary training for students and postdocs in plant genomics, bioinformatics, DNA sequencing and sequence assembly, validation, and analysis. Validated sequences of BAC contigs and sequences parsed to individual BAC clones will be deposited on a monthly basis to a project website (to be developed). All sequences will be deposited at the long-term NCBI repository and incorporated into the Gramene, GrainGenes, and MIPS comparative databases. Individual BAC clones or their groups from the nine libraries of Ae. tauschii AL8/78 and the minimal tiling path (MTP) across the contigs are publicly available and distributed through http://probes.pw.usda.gov/WheatDMarker/.