New 'super-pangenomes' project for eastern oak species

The Community Science Program proposal “Super-pangenomes for gene discovery and climate-resiliency research and breeding in eastern oak syngameons” has been approved for fiscal year 2025 by the Department of Energy's Joint Genome Institute (JGI). The proposal, led by the past Director of the Schatz Center, John Carlson, was a group effort with 33 investigators at 19 institutions. Many additional collaborators in the forest genetics community have assisted in the collection of samples for the project, including current director of the Schatz Center, Jill Hamilton.

Oaks account for a substantial portion of the carbon storage of northern temperate forests. Oaks are also important to forest product-based industries and as keystone species providing essential ecosystem services to human communities. The past success of oaks in migration and adaptation, in response to new environmental conditions following the last ice age, resulted in oaks becoming one of the most widespread, dominant, and species-rich groups of trees in northern hemisphere temperate forests. This success is also why oaks have become a focus of research into the genetic basis of adaptation to the environment in long-lived hardwood trees.

It has long been observed that closely related oak species can produce hybrid offspring when they co-exist in natural forests. For our Community Science Program project, JGI will develop a ”super-pangenome” research platform to support in-depth investigations into genetic exchange by hybridization among species within the two major sections of the oak genus - the white oaks and the red oaks. The research platform will consist of newly sequenced and assembled genomes as well as genetic diversity data for 16 oak species, 8 each in the eastern US oak white oak and red oak syngameons (groups of hybridizing species). Our existing chromosome-scale genomes, genetic linkage mapping populations, and provenance collections for Northern red oak (Quercus rubra) and white oak (Quercus alba) will serve as references in studies using the new pangenomes to identify both gene sequences and genome structural features common to and distinct among interbreeding oak species in the eastern US. With these new resources researchers will also be able to investigate in greater depth how the sharing of genes among oaks species with different environmental adaptations has contributed to the ability of oaks to adapt to past climate changes, and how that knowledge can assist in conserving and expanding the important roles of oaks in climate resiliency and generation of bio-based products. The super-pangenome research platform will also facilitate comparative genomics research into one of the persistent questions in forest genetics - how do tree species remain distinct despite frequent hybridization with related species. The pangenomes and genetic diversity data and resulting deeper knowledge base in oak genetics will also lead to genome-wide tools to guide tree improvement (breeding), conservation genetics, and oak sustainability efforts.

Carlson and Associate Professor Jesse Lasky in the Biology Department at Penn State are joined in this project by researchers at the University of Kentucky, the Morton Arboretum, Harvard University, the University of Tennessee, the US Forest Service, Purdue University, Notre Dame University, Duke University, Indiana University, the University of Missouri, Michigan Technology University, the US National Arboretum, US Geological Survey, University of Minnesota, University of Oklahoma, Auburn University, Louisiana Tech University, and the University of Maine.