Dimensions US-China: Collaborative Research: Consequences of Diversity in Asian and American Tree Syngameons for Functional Variation, Adaptation and Symbiont Biodiversity

Scope of Work NSF Supplemental- UMN, Jan 2025 Scope of Work Title: ? Dimensions US/China: Collaborative Research: Consequences of diversity in Asian and American oak syngameons for functional variation, adaptation and symbiont biodiversity PI: ? Ellen Crocker, Department of Forestry and Natural Resources, University of Kentucky Sponsor: ? NSF Dimensions of Biodiversity Project #2129237-2129236-2129281-2129312 (University of Minnesota is lead institution, PI: Jeannine Cavender-Bares) Time: 6 months A group of 3 dozen oak researchers submitted a proposal to the JGI (Joint Genome Institute) FY2025 Community Science Program (CSP) for the development of pangenome resources for characterizing hybridization and its role in adaptation in oak species. The CSP proposal (#510779), ''Super-PanGenomes for Gene Discovery and Climate-Resiliency Research and Breeding in Eastern Oak Syngameons'', was led by John Carlson (Emeritus Professor at Penn State University) as PI, and included several participants from the NSF Dimensions of Biodiversity Project (DEB award #2129237-2129236-2129281-2129312), including Jeannine Cavender-Bares at the University of Minnesota. The CSP proposal requested development of a multi-species pangenome platform encompassing annotated genome assemblies and genetic diversity data for 16 species in the white oak section and red oak section syngameons. Similarly, the NSF Dimensions of Biodiversity project, running from October 15, 2021 to October 14, 2025, focuses on evaluation of the impacts of hybridization and introgression among oak species on the extended communities of insects and microbes which oaks support. Like the CSP proposal, the approach of the NSF Dimensions of Biodiversity project includes sequencing of hundreds of samples collected from natural populations of oaks, and assembly of a new reference genome (for Quercus macrocarpa) at JGI. The CSP and NSF projects are highly complementary, and synergistic, with the new genome assemblies from the CSP project expected to provide an important new resource for the Dimensions project. The proposal was approved on 8-30-2024, and the CSP proposal team anticipated that work on the reference genome sequencing would progress quickly, as collection of samples had been completed pre-award. However, we learned that JGI requires the proposal team to provide all of the RNA preparations required for the annotation of genes in each of the 16 genomes to be assembled. This requires the team to prepare 384 RNA preparations, as JGI requires triplicate extractions from each of 8 different tissues from each of the 16 reference trees. The scientist conducting the RNA extractions at the University of Kentucky is Tetyana Zhebentyayeva, a CSP proposal Co-PI, who has substantial experience in optimizing RNA extraction protocols for tree species, including oaks. Her appointment is being supported through January 2025, by the Department of Forestry and Natural Resources at the University of Kentucky, an EPSCoR Scope of Work NSF Supplemental- UMN, Jan 2025 institution. However, RNA isolations are expected to continue through the spring 2025. The Community Science Program awards are non-financial, i.e. JGI covers internal sequencing costs but the proposal team is not provided with funds. We request supplemental funds for the NSF Dimensions of Biodiversity award to cover the unanticipated cost for the RNA extractions, including supplies and Dr. Zhebentyayeva’s salary for six months.