TRANSFORM-PGR: Whole genome assembly of the maize NAM founders

非技术摘要：玉米不仅是一种重要的作物，而且是回答植物如何生长和适应不同环境的基本问题的重要研究物种。基因组组装体是植物品种遗传信息的完整表达，是回答这些重要问题的关键资源。然而，目前只有单一类型的标本被用作玉米中大部分遗传信息的序列参考，留下了未知的玉米中许多非常有价值的自然变异。该项目将收集另外26个玉米品系的基因组，选择这些品系代表现代育种中使用的玉米品系的广泛横截面。通过添加有关基因性质以及基因组彼此如何不同的信息，序列组装将得到增强。所有信息将通过公共数据库加速发布。技术摘要：玉米是重要的作物和植物遗传学的模式生物。然而，目前几乎所有形式的序列分析都涉及单个B73近交系。除了B73之外，研究最广泛的玉米品系是被称为NAM创始品系的25个自交系的核心组，其代表了现代玉米多样性的广泛横截面。先前的数据表明，基因含量在不同品系之间的差异可以超过5%，并且多达一半的功能遗传信息位于基因之外的高度可变的基因间空间中。为了捕获和利用这种变异，将使用配对策略对NAM建立者近交系和含有异常染色体10的第二十六个品系进行测序和组装。支架将通过BioNano光学映射进行验证，并使用连接数据进行排序和定向。来自多个组织的RNA-seq数据将用于注释每个基因组，组装和注释将通过MaizeGDB，NCBI和Cyverse的基因组浏览器支持发布。比较基因组工具将用于鉴定和编目玉米泛基因组，并评估结构变异如存在-不存在变异和拷贝数变异在确定农艺性状中的作用。结果将通过项目网站和CyVerse/Gramene/MaizeCODE研讨会在2019年3月的第61届玉米年会上传播。

Non-Technical Abstract: Maize is not only an important crop but an important study species for answering basic questions about how plants grow and adapt to different environments. Genome assemblies, which are complete representations of the genetic information in a plant variety, are critical resources for answering these important questions. However, currently only a single type specimen is used as the sequence reference for most of the genetic information in maize, leaving unknown much of the highly valuable natural variation in maize. This project will assemble the genomes of 26 additional maize lines, chosen to represent a broad cross section of the maize lines used in modern breeding. The sequence assemblies will be enhanced by adding information about the nature of the genes and how the genomes differ from each other. All information will be released on an accelerated schedule through public databases. Technical Abstract: Maize is an important crop and model organism for plant genetics. However, currently nearly all forms of sequence analysis are referenced to the single B73 inbred. Beyond B73, the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds and a twenty-sixth line containing abnormal chromosome 10 will be sequenced and assembled using a mate-pair strategy. Scaffolds will be validated by BioNano optical mapping, and ordered and oriented using linkage data. RNA-seq data from multiple tissues will be used to annotate each genome, and assemblies and annotations will be released with genome browser support through MaizeGDB, NCBI, and Cyverse. Comparative genomic tools will be used to identify and to catalog the maize pangenome, and to assess the role of structural variation such as presence-absence variation and copy number variation in the determination of agronomic traits. Results will be disseminated through a project web site and a CyVerse/Gramene/MaizeCODE Workshop at the 61st Annual Maize Meeting in March of 2019.