Gene Discovery in the Cereals

PI: W. Richard McCombie（冷泉港实验室）Co PI: Doreen Ware（冷泉港实验室）主要合作者：Robert A. Martienssen（冷泉港实验室）基因组序列数据有望极大地促进对基础植物科学的理解，并催化植物育种的实际进展。虽然基因组的“完整”、连续、“碱基完美”序列是基因组计划最有用的结果，但在大多数应用中并不是必需的。此外，对于非常大的基因组或大量中等大小的基因组，碱基完美序列在时间和成本方面都是令人望而却步的。然而，最近的技术进步和即将广泛可用的技术为植物基因组学提供了一个有吸引力的选择。本项目旨在利用下一代序列技术，对小麦（AA、AABB和DD基因组含种）和六倍体小麦（中国春）三个密切相关的祖先基因组中的绝大多数基因进行鉴定。每个基因组将使用Illumina测序仪（配对末端100个碱基读数）测序到约50倍的覆盖率，使用Pacific biosciences测序技术测序到约8 -10倍的覆盖率。此外，该项目将在太平洋生物科学仪器上对每个基因组进行远程“频亮”读取，这将达到约2tb的原始序列。这些序列将被组装和注释，以最大限度地为更广泛的科学界所用。所有原始数据、程序集和注释一经生成并经过质量检查，就会在可能进行的任何发布之前向公众发布。该项目更广泛的影响是通过向更广泛的谷物研究界提供约2tb的原始基因组序列数据，以及大量谷物基因组中绝大多数基因的组装和注释，解决数据可用性问题。预计这些数据的获取将从根本上加速小麦功能基因组学的研究。本项目生成的所有数据均可通过项目网站GenBank和iPlant Collaborative （http://www.iplantcollaborative.org/）访问。此外，项目更新将与国际小麦基因组测序联盟（IWGSC）协调，并在（http://www.wheatgenome.org/Projects）和GrainGenes （http://wheat.pw.usda.gov/GG2/index.shtml）上提供。

PI: W. Richard McCombie (Cold Spring Harbor Laboratory) Co PI: Doreen Ware (Cold Spring Harbor Laboratory)Key Collaborator: Robert A. Martienssen (Cold Spring Harbor Laboratory)Genomic sequence data holds the promise of dramatically advancing both the understanding of basic plant science, and of catalyzing practical advances in plant breeding. While the "complete", contiguous, "base perfect" sequence of a genome is the most useful outcome of a genome project, it is not necessary for most applications. Furthermore, base perfect sequence is prohibitive in terms of both time and cost for very large genomes or large numbers of moderately sized genomes. However, recent technological advances and soon-to-be broadly available technologies provide an attractive option for plant genomics. This project seeks to use next generation sequence technologies to identify the vast majority of genes in three closely related progenitor genomes of wheat (AA, AABB, and DD genome containing species) and hexaploid wheat (Chinese spring). Each genome will be sequenced to about 50x coverage with Illumina sequencers (paired end 100 base reads) and to about 8x-10x coverage using the Pacific Bio-Sciences sequencing technology. In addition, the project will sequence each genome with long range "strobe" reads on the Pacific Biosciences instrument that will amount to about 2 terabases of raw sequence. The sequences will be assembled and annotated for maximum use by the broader scientific community. All raw data, assemblies, and annotations will be released to the public as soon as they are generated and quality checked and prior to any publication that might be pursued. The broader impact of this project is to solve the data availability problem by providing about 2 terabases of raw genome sequence data to the broader cereal research community as well as the assemblies and annotation of the vast majority of genes in a large number of cereal genomes. It is expected that access to these data will radically accelerate functional genomics in wheat. All data generated in this project can be accessed through the project website, GenBank, and through the iPlant Collaborative (http://www.iplantcollaborative.org/). In addition, project updates will be coordinated with the International Wheat Genome Sequencing Consortium (IWGSC) and made available at (http://www.wheatgenome.org/Projects) and at GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml).