Sequencing and Annotating the Valley Oak Genome

首席研究员：维多利亚·索尔克（加州大学洛杉矶分校）首席研究员：Matteo Pellegrini（加州大学洛杉矶分校），Paul Gugger（马里兰大学环境科学中心，阿巴拉契亚实验室），Steven Salzberg（约翰·霍普金斯大学）Shawn Cokus和Sorel Fitz-Gibbon（加州大学洛杉矶分校）：橡树是北美生态系统中生物量最多的树种，为社会提供了重要的经济和生态系统价值。山谷橡树是加州生物多样性的关键物种，它为基因组工具的开发提供了一个很好的研究系统，可以为经济利用、保护、碳封存和恢复受气候变化威胁的弹性森林的管理提供信息。该项目将生成高质量的谷栎基因组序列，并对基因组不同部分的结构和功能进行注释，为科学界和资源管理者提供智力资源。这些数据将有助于研究整个北半球橡树的森林遗传学家，也将为适应气候的进化提供新的见解，并有助于目前对基因组哪些部分在适应不同环境中很重要的理解，以及哪些部分在气候变化下管理橡树林提供重要信息。同一物种内的植物在异质环境中生长的能力是植物科学的一个主要课题。考虑到气候变化的快速速度，长寿植物种群对这些变化的反应能力是一个紧迫的问题。该项目的主要目标是利用最先进的全基因组测序方法开发基因组资源，以了解山谷橡树（Quercus lobata）对不同环境的本地适应性，并为更广泛的科学界和自然资源管理者提供资源。利用加州橡树的独特特征，该项目将(1)提供一个完整的、高质量的山谷橡树基因组序列，包括基因区域和重复元件的结构和功能注释；(2) 190株自然种群的全基因组序列和全基因组单核苷酸多态性（SNP）数据；(3)气候环境下自然选择的候选SNP，这将有助于理解当地对气候的适应，并进一步提供与环境适应相关的注释。除了解决单个植物如何适应不同气候的基本问题外，长期意义在于该项目将提供关于基因组多样性如何应对气候条件变化的新知识。该项目产生的资料将通过NCBI、Dendrome (dendrome.ucdavis.edu/),)以及新创建的橡树基因组网站和FTP网站（valleyoak.ucla.edu）向公众提供。

PI: Victoria Sork (University of California-Los Angeles)CoPIs: Matteo Pellegrini (University of California-Los Angeles), Paul Gugger [University of Maryland Center for Environmental Science (UMCES), Appalachian Laboratory] and Steven Salzberg (Johns Hopkins University) Senior Personnel: Shawn Cokus and Sorel Fitz-Gibbon (University of California-Los Angeles)Oak trees, which contain more biomass in North American ecosystems than any other tree genus, provide major economic and ecosystem value to society. Valley oak, a keystone species for biodiversity in California, provides an excellent study system for the development of genomic tools that can inform management for economic use, conservation, carbon sequestration, and restoration of resilient forests threatened by climate change. This project will produce a high quality genome sequence for valley oak and annotate the structure and functions of different parts of the genome as an intellectual resource for the scientific community and resource managers. The data will be helpful to forests geneticists working on oaks throughout the Northern Hemisphere, and it will also provide new insight about the evolution of adaptation to climate and contribute to the current understanding of which parts of the genome are important in adaptations to different environments, and which provide information important in managing oak forests under climate change. The ability of plants within the same species to grow across heterogeneous environments is a major topic for plant science. Given the rapid rate of climate change, the ability of long-lived plant populations to respond to these changes is an urgent question. The major goal of this project is to use state-of-the art whole-genome sequencing approaches to develop genomic resources for understanding local adaptation of valley oak (Quercus lobata) to different environments, as well as provide a resource to the broader scientific community and natural resource managers. Taking advantage of unique features of this keystone California oak, this project will (1) provide a complete, high-quality sequence of the valley oak genome with structural and functional annotations of genic regions and repetitive elements; (2) whole-genome sequences and genome-wide single-nucleotide polymorphism (SNP) data from 190 trees from natural populations, and (3) candidate SNPs that are under natural selection along climate environments, which will contribute to understanding local adaptation to climate and provide further annotations relevant to environmental adaptations. In addition to addressing the fundamental question of how individual plants adapt to different climates, a long-term significance is that the project will provide new knowledge on how genomic diversity can respond to changing climate conditions. The materials generated in this project will be made publically available through NCBI, Dendrome (dendrome.ucdavis.edu/), and a newly created oak genome website and FTP site (valleyoak.ucla.edu).