Sequencing the Aegilops tauschii Genome

合作者：Jan Dvorak(加州大学戴维斯分校)、Ktrien M.Devos(佐治亚大学，雅典)、Steven Salzberg(约翰·霍普金斯大学)、Yong Q.Gu和Olin D.Anderson(USDA-ARS，奥尔巴尼/加州大学戴维斯分校)合作者：Hans-Georg Müler(加州大学戴维斯分校)，Jeffrey L.Bennetzen(佐治亚大学，雅典分校)，刘志勇(中国农业大学，北京)，Philippe Leroy(INRA/IBP，法国)，Eric Lyons和Carol Soderlund(亚利桑那大学，图森)马正强(南京农业大学，中国)，龙茂(中国农业科学院)，Klaus F.X.Mayer(德国慕尼黑Helmholtz中心)，Richard W.McCombie(冷泉港实验室)，孙启新(西北A&AMP；托马斯·威克尔(瑞士苏黎世大学)和Frank M.You(加拿大温尼伯农业和农业食品公司)面包小麦是全球粮食供应所依赖的三大支柱之一。尽管小麦具有特殊的重要性，但由于其杂交起源(多倍体)及其庞大的基因组大小，高质量的小麦基因组草稿序列是无法获得的。为了协助国际面包小麦基因组测序工作，将制作高质量的节节麦基因组草图，节节麦是面包小麦的三个祖先之一。Ae的巨大体积和巨大复杂性。为了产生高质量的基因组序列草稿，需要采用有序克隆测序策略。这一战略将涉及对大约50,000个含有Ae大片段的细菌人工染色体(BAC)克隆进行测序。Tauschii DNA已经被命令代表Ae中的核苷酸的连续序列。结节草属染色体DNA。BAC克隆池将使用下一代DNA测序平台进行测序，并组装成长的连续序列。组装的序列的正确性将通过一种新的光学纳米技术来验证。组装的序列中的基因和转座元件将被注释。通过这种方式，Ae中所有基因和转座元件的序列、位置和方向。结节鸟的基因组将会被确定。禽流感最直接的影响是。该项目产生的节节麦基因组序列将用于预测基因在小麦及其近缘物种中的位置，从而加快小麦及其近缘物种基因组测序的进展，并通过传统的育种方法和生物技术促进这些物种的基因发现和操作。Ae.在分析小麦起源以来小麦基因组发生的变化时，tauschii基因组序列将作为参考，为理解禾草基因组结构和进化提供重要的基础性贡献。草案基因组序列中预测的3.6万多个基因与生物功能的关联将是一项艰巨的任务。出于这个原因，该项目将吸引对分析Ae基因感兴趣的大型研究社区。Tauschii以社区为基础的手动基因注释和项目数据库中的图形汇编结果。为了最大限度地提高小麦育种者和其他利益攸关方对项目资源的认识，将在小麦育种者参加的专业会议上定期介绍/举办这些资源研讨会。该项目还将在植物基因组学、生物信息学、DNA测序和序列组装、验证和分析方面为学生和博士后提供出色的跨学科培训。经验证的BAC重叠群序列和解析到单个BAC克隆的序列将按月存放到项目网站(待开发)。所有序列将存放在长期NCBI储存库，并纳入Gramene、GrainGenes和MIPS比较数据库。Ae的九个文库中的单个BAC克隆或它们的组。Tauschii AL8/78和跨重叠群的最小平铺路径(MTP)是公开提供的，并通过http://probes.pw.usda.gov/WheatDMarker/.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/.