Sequencing and Annotating the Valley Oak Genome

Pi：Victoria Sork(加州大学洛杉矶分校)Copis：Matteo Pellegrini(加州大学洛杉矶分校)，Paul Gugger[马里兰大学环境科学中心(UMCES)，阿巴拉契亚实验室]和Steven Salzberg(约翰霍普金斯大学)高级人员：Shawn Cokus和Sorel Fitz-Gibbon(加州大学洛杉矶分校)橡树在北美生态系统中含有比其他树种更多的生物量，为社会提供了主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极好的研究系统，这些工具可以为经济使用、保护、碳固存和恢复受气候变化威胁的弹性森林的管理提供信息。该项目将为山谷橡树生产高质量的基因组序列，并注释基因组不同部分的结构和功能，作为科学界和资源管理者的智力资源。这些数据将有助于整个北半球研究橡树的森林遗传学家，它还将为适应气候的进化提供新的见解，并有助于目前了解基因组的哪些部分在适应不同环境方面起重要作用，以及哪些部分提供了在气候变化下管理橡树林的重要信息。植物在同一物种中跨越异质环境生长的能力是植物科学的一个主要主题。鉴于气候变化的速度如此之快，长寿植物种群应对这些变化的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)对不同环境的局部适应，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性，该项目将(1)提供完整、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)来自自然种群的190棵树的全基因组序列和全基因组单核苷酸多态(SNP)数据；(3)沿气候环境处于自然选择状态下的候选SNP，这将有助于了解当地对气候的适应，并提供与环境适应相关的进一步注释。除了解决单个植物如何适应不同气候的根本问题外，该项目的长期意义在于，该项目将提供关于基因组多样性如何应对不断变化的气候条件的新知识。该项目产生的材料将通过NCBI、Dendrome(endrome.ucdavis.edu/)以及新创建的橡树基因组网站和ftp网站(valley oak.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).