1,001 (Epi) Genomes Project

智力优势：植物生物学家需要在每个物种中有许多完全测序和功能注释的基因组，以充分利用进化的力量，并了解生物体如何运作和适应其环境。该项目将有助于从1000多个拟南芥近交品系中生成基因组DNA序列的国际努力，同时推动DNA测序本身的硬件和软件开发的技术发展，以使序列数据有意义。具体来说，这个项目将生成基因组、转录组和甲基组序列。基因组序列将为拟南芥的单倍型结构和结构变异提供一个无与伦比的视角。转录组序列数据将有助于基因组注释和鉴定自然发生的剪接异构体。最后，DNA甲基组测序数据将允许在人群范围内鉴定外显子变异。这三个测序数据集（遗传、转录和DNA甲基组）将很好地相互吻合，以提供拟南芥种群内的一套全面的变异。结合种群或物种内不同个体的遗传、表观遗传和转录变异，将为通过数量性状位点定位或全基因组关联研究分析表型多样性提供潜在的来源。此外，这些数据将通过对拟南芥菌株的实验操作，使后续的机制研究成为可能，并将补充个人研究人员的努力，这些研究人员正在使用相同的资料对数千个性状的表型进行编目。更广泛的影响：本项目将在两大领域产生影响。首先，计划研究的完成将为植物生物界带来重要的新资源：物种内遗传、表观遗传和转录变异的大规模信息。所有的DNA、胞嘧啶甲基化和RNA序列数据将免费提供给研究界。这些使能工具和技术对农业和林业的长期影响预计将是深远的，为构建具有优良农艺性状的植物新品种提供基础知识。该项目同样重要的一个方面是培训，培训将在各个层面提供，包括向高中生、本科生和研究生以及博士后提供指导。

Intellectual merit: Plant biologists need many completely sequenced and functionally annotated genomes within each species to fully exploit the power of evolution and to understand how an organism functions and adapts to its environment. This project will contribute to an international effort aimed at generating genomic DNA sequences from over 1,000 inbred strains of Arabidopsis thaliana, while driving technology developments in both the hardware for the DNA sequencing itself and in software development to make sense of the sequence data. Specifically, this project will generate genome, transcriptome, and methylome sequences. The genome sequences will provide an unparalleled view of haplotype structure and structural variation for Arabidopsis thaliana. The transcriptome sequence data will assist in genome annotation and identification of naturally occurring splice isoforms. Lastly, the DNA methylome sequencing data will permit identification of epiallelic variation on a population-wide level. These three sequencing data sets (genetic, transcriptional and DNA methylomes) will dovetail nicely with each other to provide a comprehensive set of variants within the Arabidopsis thaliana population. Combining genetic, epigenetic and transcriptional variation from different individuals in a population or within a species will provide a potential source for analyzing phenotypic diversity via quantitative trait loci mapping or genome-wide association studies. Moreover, these data will enable subsequent mechanistic studies through experimental manipulation of Arabidopsis thaliana strains and will complement the efforts of individual investigators who are using the same accessions to catalog phenotypes for thousands of traits. Broader impacts: The impact of this project will be in two broad areas. First, the completion of the planned research will result in important new resources for the plant biology community: large-scale information on genetic, epigenetic and transcriptional variation within a species. All of the DNA, cytosine methylation and RNA sequence data will be made freely and easily accessible to the research community. The long-term impact of these enabling tools and technologies on agriculture and forestry is expected to be profound, providing fundamental knowledge for the construction of new plant varieties with superior agronomic traits. An equally important aspect of this program is training, which will be provided at a variety of levels, including outreach to high school, undergraduate and graduate students as well as postdoctoral mentoring.