March 12, 2024

To Campus Sustainability Fund:

I am writing to express intent to apply to the Large Grants program to fund a project entitled "Revealing the heritage and evolution of UW Yoshino Cherries through whole genome sequencing", referred to as the "Yoshino Sequencing Project" below. We aim to obtain $15,496 to sequence the genomes of four cherry trees from the Quad, and to use genetic analysis to relate the iconic trees with original "Somei-Yoshino" clones from Japan.

Cherry trees have complex patterns of speciation and hybridization (Baek et al. 2018). Yoshino cherries (Prunus yedoensis) are especially complex as the "species" in fact represents a hybrid between two parents, P. speciosa and maternal P. pendula f. ascendens (Takenaka 1963). The “Somei-Yoshino” cultivar was originally planted by clonal propagation across Japan in the late 1800s and sequenced in 2019 (Shirasawa et al. 2019). The most recent genomic analyses indicate that just 4 clones have given rise to most Yoshino cherries today (Shirasawa et al. 2023).

Experts believe the UW Cherries are "Somei-Yoshino" clones originally given as a gift from Japan in the 1930s. However, records from their original 1936 planting at the Canal Reserve have been lost (Shiotani 2017). Thus, despite their fame and reputation, there is no direct evidence that the trees are the precise “Somei-Yoshino” cultivar, or regarding the clonal lineage from which the trees derive. Plant genomes now provide the opportunity to definitively identify our trees’ provenance. Two recent publications make available genome data from 140 species and hybrids of cherry trees, including 46 clones of "Somei-Yoshino" (Shirasawa et al. 2019, 2023). By sequencing the genomes of four individual trees from the Quad, and relating this data to tree genomes from Japan, we will be able to definitively state the clonal identity of our iconic trees, and potentially even determine their provenance going back to original specimens from Ueno Park in Tokyo.

The Steinbrenner lab (https://steinbrennerlab.org) in the Department of Biology at the University of Washington is well equipped to perform this work. Our lab studies the evolution of plant immunity genes. We are interested to begin studying genetic changes which accumulate over long life cycles of trees. The age and clonal descendants of the UW Cherries make them a perfect model for studying trajectories of immunity in long-lived plants. In addition, we already host undergraduate students each summer on National Science Foundation-funded research internships relating to plant genome analysis. We will request summer stipend funding to support the work of one summer undergraduate student, who will be directly responsible for genome assembly steps in our Yoshino Sequencing Project. The student would participate as a full member of the lab for a 10-week paid internship in the summer of 2024.

We will integrate findings with a broader project entitled "American Campus Tree Genomes" (https://www.hudsonalpha.org/learning-from-the-trees/), with Dr. Alex Harkess of the HudsonAlpha laboratory as the lead collaborator. HudsonAlpha will provide genome sequencing and analysis services for the project, while the CSF Yoshino Sequencing Project grant will cover reagent costs. Dr. Harkess has an established track record of involving undergraduate co-authors in published genome sequencing projects.

The Steinbrenner lab will recruit an upper-division Biology major from my genetics and genomics courses (BIOL400 / BIOL426) to participate in a formal internship to assist with the Yoshino Sequencing Project. The student will participate in a formal internship program in Plant Genetics and Genomics organized by the Steinbrenner lab, including the opportunity to participate in career development workshops organized by the UW Louis Stokes Alliance for Minority Participation.

For outreach materials we are coordinating with Campus Arborist Sara Shores (shoress@uw.edu) and Brockman Tree Tour organizer Theo Hoss (theodore.hoss@outlook.com). UW Graduate students in the Biology department will also assist with the project as an outreach and educational component of their training. Student participants will develop outreach materials such as signage, webpages, and a springtime event to share our findings with UW Quad visitors, promoting the heritage of our most famous campus trees.

Please find attached a timeline, references, and budget. I look forward to hearing back from the CSF.

References:

• Baek, S., Choi, K., Kim, GB. et al. Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries. Genome Biol 19, 127 (2018). https://doi.org/10.1186/s13059-018-1497-y
• Kenta Shirasawa, Tomoya Esumi, Hideki Hirakawa, Hideyuki Tanaka, Akihiro Itai, Andrea Ghelfi, Hideki Nagasaki, Sachiko Isobe, Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis), DNA Research, Volume 26, Issue 5, October 2019, Pages 379–389, https://doi.org/10.1093/dnares/dsz016
• Kenta Shirasawa, Tomoya Esumi, Akihiro Itai, Katsunori Hatakeyama, Tadashi Takashina, Takuji Yakuwa, Katsuhiko Sumitomo, Takeshi Kurokura, Eigo Fukai, Keiichi Sato, Takehiko Shimada, Katsuhiro Shiratake, Munetaka Hosokawa, Yuki Monden, Makoto Kusaba, Hidetoshi Ikegami, Sachiko Isobe. Propagation path of a flowering cherry (Cerasus × yedoensis) cultivar ‘Somei-Yoshino’ traced by somatic mutations. bioRxiv 2023.07.11.548633; doi: https://doi.org/10.1101/2023.07.11.548633
• Shiotani, Yuki . History of the Cherry Trees in the Liberal Arts Quadrangle at the University of Washington. 2018; Exchange Thesis Project.
• Takenaka Y. The origin of the Yoshino cherry tree. J Hered. 1963;54:207–11.