Sequencing the Maize Genome

PI: Richard K. Wilson，博士，华盛顿大学Sandra Clifton博士，华盛顿大学圣路易斯分校Rod Wing博士，亚利桑那大学Patrick Schnable博士，爱荷华州立大学Srinivas Aluru博士，爱荷华州立大学Lincoln Stein博士，医学博士，冷泉港实验室Doreen Ware博士，冷泉港实验室W. Richard McCombie博士，冷泉港实验室Robert Martienssen博士，冷泉港实验室玉米是一个重要的生物研究体系，有着悠久而丰富的历史。在过去的一个世纪里，围绕着广泛的遗传工具和多样的种质资源，一个活跃的研究团体已经成长起来。在这段时间里，玉米已经成为解决遗传学基本问题的主要系统，如驯化对基因组结构的影响，杂种优势的分子基础（杂交活力），以及转座子在基因组进化中的作用。对玉米的研究使我们对植物基本生命过程的理解取得了重大进展，如繁殖、种子形成、萌发、光合作用以及氨基酸、碳水化合物和脂肪酸等初级代谢物的生物合成。基因组测序是一个合乎逻辑的下一步，可以使玉米作为一种实验系统得到最佳利用，并将研究成果转化为改良作物。玉米基因组有26亿个碱基对，其大小与人类基因组差不多。然而，它的组织结构要复杂得多。超过80%的基因组是由重复DNA的复杂混合物组成的，其中包括几种反转录转座子。只有大约20%的基因组包含这些基因，这些基因分散在小岛上的10条染色体中。与基因图谱相关联的详细物理图谱已经开发出来，覆盖了90%以上的基因组。基于对基因组结构和组织的详细了解，玉米研究界已经制定了基因组序列的“黄金标准”描述（http://www.maizegdb.org/genome/goldstandard.pdf）。黄金标准玉米基因组被定义为包含所有玉米基因的完整序列和结构及其在玉米遗传图谱和物理图谱上的位置（按线性顺序），以B73作为参考基因组。该项目旨在利用现有技术提供尽可能接近金标准的玉米基因组序列。对物理图谱上已知位置的细菌人工染色体（BAC）克隆进行6倍覆盖测序，并与先前通过表达序列标签（est）、转座子插入位点、基因富集基因组DNA和全基因组鸟枪文库测序获得的可用序列信息进行整合。所得到的基因组序列将包含包含基因和调控元件的非重复区域的高质量序列（每10万个碱基中少于一个错误），锚定在遗传和物理图谱上。该序列将被注释为基因模型、预测的外显子/内含子结构、EST和全长cDNA数据、基因本体以及与其他生物序列的同源性。华盛顿大学圣路易斯基因组测序中心将与圣路易斯科学中心合作，针对K-12学生及其家长开展以玉米和基因组序列为重点的教育活动。将通过设在冷泉港实验室的Gramene （http://www.gramene.org）为研究人员、学生和育种者开发适合玉米序列最终用户的培训资源、教程和讲习班。所有长度超过2,000碱基对的初级和组装序列将在生成24小时内存入GenBank （http://www.ncbi.nlm.nih.gov/Genbank/）。跟踪文件将在生产后一周内存入NCBI跟踪存储库（http://www.ncbi.nlm.nih.gov/Traces/trace.cgi）。组装完成的BAC克隆序列一旦通过所有质量分析测试并经质量分析团队批准提交，将存入GenBank。项目信息和数据将通过华盛顿大学基因组测序中心的网站（http://www.genome.wustl.edu）提供。玉米序列汇编和玉米遗传资源将按季度纳入Gramene （http://www.gramene.org）和MaizeGDB （http://www.maizegdb.org）。玉米（玉米）是美国最重要的经济作物之一。2004年，种植了8090万英亩玉米，产值超过220亿美元。虽然玉米在美国是作为食品和饲料种植的，但它也被转化为无数的加工食品，并作为许多工业产品的重要材料。玉米基因组序列将成为公共和私营部门继续利用玉米作为推进基础生物学以及开发玉米新品种和改良品种的实验系统的关键资源。本项目是玉米基因组测序项目的一部分：NSF/DOE/USDA联合项目。

PI: Richard K. Wilson, Ph.D., Washington UniversityCo-PIs: Dr. Sandra Clifton, Ph.D., Washington University St. Louis Dr. Rod Wing, Ph.D.,University of Arizona Dr. Patrick Schnable, Ph.D.,Iowa State University Dr. Srinivas Aluru, Ph.D.,Iowa State University Dr. Lincoln Stein, M.D. Ph.D., Cold Spring Harbor Laboratory Dr. Doreen Ware, Ph.D., Cold Spring Harbor Laboratory Dr. W. Richard McCombie, Ph.D., Cold Spring Harbor Laboratory Dr. Robert Martienssen, Ph.D., Cold Spring Harbor Laboratory Maize is an important biological research system with a long and rich history. Over the past century, an active research community has grown up around the available extensive genetic tools and diverse germplasm. In this time, maize has become a leading system for addressing fundamental questions in genetics such as the impact of domestication on genome structure, the molecular basis of heterosis (hybrid vigor), and role of transposons in genome evolution. Research on maize has led to major advances in our understanding of fundamental life processes in plants such as reproduction, seed formation, germination, photosynthesis, and biosynthesis of primary metabolites including amino acids, carbohydrates and fatty acids. A genome sequence is a logical next step to enable the best use of maize as an experimental system and in order to translate research advances into improved crops. At 2.6 billion base pairs, the maize genome is about the same size as the human genome. However, its organization is far more complex. More than 80% of the genome is made up of a complex mixture of repetitive DNA that includes several classes of retrotransposon. Only about 20% of the genome comprises the genes and these are scattered throughout the 10 chromosomes in small islands. A detailed physical map that is linked to the genetic map has been developed that covers more than 90% of the genome. Based on this detailed knowledge about the genome structure and organization, the maize research community has developed a description of the "gold standard" for a genome sequence (http://www.maizegdb.org/genome/goldstandard.pdf). The gold standard maize genome is defined as containing the complete sequence and structures of all maize genes and their locations (in linear order) on both the genetic and physical maps of maize, using B73 as the reference genome.This project is designed to provide a maize genome sequence as close to the gold standard as possible with the currently available technology. Bacterial Artificial Chromosome (BAC) clones of known location along the physical map will be sequenced to 6x coverage, and integrated with the available sequence information obtained through prior sequencing of Expressed Sequence Tags (ESTs), transposon insertion sites, gene-enriched genomic DNA and whole genome shotgun libraries. The resulting genome sequence will contain high quality sequence (fewer than one error per 100,000 bases) of the non-repetitive regions that include the genes and regulatory elements, anchored to the genetic and physical maps. The sequence will be annotated for gene models, predicted exon/intron structures, EST and full-length cDNA data, gene ontologies, and homologies with sequences from other organisms.Educational activities that focus on maize and the genome sequence and aimed at K-12 students and their parents will be developed at Washington University St. Louis Genome Sequencing Center in collaboration with the St. Louis Science Center. Training resources, tutorials and workshops for end-users of the maize sequence appropriate for researchers, students, and breeders will be developed and made available through Gramene (http://www.gramene.org) located at the Cold Spring Harbor Laboratory. All primary and assembled sequences over 2,000 base pairs in length will be deposited in GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) within 24 hours of generation. Trace files will be deposited in the NCBI Trace Repository (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) within one week of production. Assembled, finished BAC clone sequences will be deposited in GenBank as soon as the finished sequence has passed all quality analysis tests and has been approved for submission by the quality analysis team. Project information and data will be available through a web site accessible through the Washington University Genome Sequencing Center (http://www.genome.wustl.edu). Maize sequence assemblies and maize genetic resources will be incorporated into Gramene (http://www.gramene.org) and MaizeGDB (http://www.maizegdb.org) on a quarterly basis. Maize (corn) is one of the most economically important plants in the US. In 2004, 80.9 million acres of corn were planted with a production value of over $22 billion. While corn is grown in the U.S. for food and feed, it is also converted into a myriad of processed food products and serves as an important material for many industrial products. The maize genome sequence will be a key resource for continued use of maize as an experimental system for advancing fundamental biology as well as for the development of new and improved maize varieties in the public and private sector.This project was funded as part of the Maize Genome Sequencing Project: An NSF/DOE/USDA Joint Program.