Sequencing and Annotating the Valley Oak Genome

University Of California-Los Angeles, Los Angeles CA

Investigators

Abstract

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).