At a glance
We propose to sequence the genomes of our iconic Yoshino cherry trees on the Quad. By analyzing the genetic information we… Read full summary
- Funding received
- 2023-2024
- Large
- Awarded
- $16,500
- Funding partners
-
- Student Activities Fee (SAF)
We propose to sequence the genomes of our iconic Yoshino cherry trees on the Quad. By analyzing the genetic information we will be able to trace the trees back to original clonal varieties from Japan, and we will generate flyers and a presentation about the heritage and conservation of the cherries in the future. The findings will promote campus community around the cherry blossom season, will contribute to a broader nationwide project to sequence American Campus Tree Genomes (ACTG), and will train an undergraduate student intern in modern genomic techniques through the Steinbrenner lab in UW Biology (www.steinbrennerlab.org). In addition to Professor Steinbrenner's laboratory, the project will involve the Campus arborist, visitor center, volunteers with the Brockman Campus Tree Tour, and the HudsonAlpha Institute for Biotechnology.
We propose to sequence the genomes of our iconic Yoshino cherry trees on the Quad. By analyzing the genetic information we will be able to trace the trees back to original clonal varieties from Japan, and we will generate flyers and a presentation about the heritage and conservation of the cherries in the future. The findings will promote campus community around the cherry blossom season, will contribute to a broader nationwide project to sequence American Campus Tree Genomes (ACTG), and will train an undergraduate student intern in modern genomic techniques through the Steinbrenner lab in UW Biology (www.steinbrennerlab.org). In addition to Professor Steinbrenner’s laboratory, the project will involve the Campus arborist, visitor center, volunteers with the Brockman Campus Tree Tour, and the HudsonAlpha Institute for Biotechnology.
Adam Steinbrenner
Project lead
- astein10@uw.edu
- Affiliation
- Faculty
-
Team member
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.
Request amount and budget
How the project will react to funding reductions
10% to 20% cuts would change the project by resulting in smaller stipends to the student intern. The project would not be possible with a 50% cut as the DNA sequencing line items are required by our collaboration partners in the American Campus Tree Genomes project.
Plans for financial longevity
Professor Steinbrenner will be responsible to maintain public access to all presentations, flyers, and billboard materials in future years. He will coordinate with future representatives of the Brockman Campus Tree Tour, Visitor Center, and Arborist office. He will be available to the public and to any media inquiries.
Problem statement
The longevity of the Yoshino cherry trees on the Quad, and the broader cherry tree population on campus, is critically important for our campus community. Genomic data on the trees will allow us to infer if they are well adapted to climate change conditions in the Pacific Northwest, especially relative to other cherry varieties. If Quad trees need to be replaced in the future, the genomic data will be used to inform efforts to have cherry biodiversity among the replacement trees.
Measure the impacts
Outreach to the general public will be measured through QR code scans, website metrics such as length-of-visit, and number of flyers distributed. Attendance to public presentations in cherry blossom season will be measured.
The mentorship of the student intern will be measured through a qualitative survey for before-after outcomes of the research internship. A 1-5 Likert scale will be used to measure technical confidence, communication skills, and scientific self-identity. Open ended comments will be gathered to inform the training of future scientific interns in the UW Biology department.
Education and outreach goals
The student intern will be responsible to create flyers, billboards, and a presentation to raise awareness about the heritage and evolution of these iconic trees. The outreach efforts will available for future cherry blossom events each March, when the cherry trees are in full bloom and attract numerous visitors to the campus.
Flyers will be created to provide detailed information about the Yoshino Sequencing Project, including the historical significance of the cherry trees, the scientific methods being employed, and the preliminary findings from the genetic analyses. These flyers will be distributed throughout the campus and surrounding community to both students and local residents. The flyers will be designed to be visually appealing and easy to understand, featuring images of the cherry blossoms and infographics that explain the genetic sequencing process.
In addition to flyers, billboards will be strategically placed around the Quad and key locations on campus to capture the attention of a broader audience. These billboards will highlight the main objectives of the project, the collaboration with the HudsonAlpha Institute, and the importance of preserving the genetic heritage of the Yoshino cherries. The billboards will be available for years after the initial project and will encourage the public to learn more about the genetic research and its implications for biodiversity and conservation.
Presentations will be a cornerstone of the outreach efforts, particularly during the annual cherry blossom event in March. The project team, including undergraduate and graduate students from the Steinbrenner lab, will host a series of public talks and interactive sessions to share their findings and engage with the audience. These presentations will cover the historical background of the Yoshino cherry trees, the scientific techniques used in the project, and the preliminary results of the genetic analyses. By involving the community in these educational events, the project aims to foster a deeper appreciation for the cherry trees and the scientific research being conducted.
Through these comprehensive outreach strategies, the Yoshino Sequencing Project aims to create a well-informed and engaged community that appreciates the cultural and scientific significance of the cherry trees at the University of Washington. The combination of flyers, billboards, and presentations will ensure that the message reaches a wide audience, promoting awareness and support for the ongoing genetic research and the preservation of these cherished trees.
Student involvement
An undergraduate student intern will play a crucial role in the "Yoshino Sequencing Project," working directly under the guidance of both the Steinbrenner lab at UW Biology and a collaborating laboratory, the Harkess lab at HudsonAlpha (Huntsville, AL). The intern’s responsibilities will encompass various stages of the project, from sample collection to data analysis and outreach activities. The intern will be an upper-division Biology major recruited from the genetics and genomics courses taught by Professor Steinbrenner (BIOL400 / BIOL426). The intern will be paid a $5000 stipend to work full-time in the Steinbrenner lab in the summer of 2025.
If recruited before Fall 2024, the intern will assist in the collection of tissue samples from the cherry trees in the University of Washington Quad. This will involve careful documentation and handling of the samples to ensure their integrity for subsequent genomic analyses, in collaboration with UW Arborist Sara Shores. The intern will then participate in the preparation of high-molecular weight DNA isolations, a critical step that will be optimized with support from the Harkess lab. Quality control measures for both DNA and RNA isolations will be conducted to ensure the samples meet the standards required for sequencing.
In 2025, the intern will be involved in the genome assembly process. They will work with data generated by the Harkess lab, learning to assemble and annotate the genomes of the cherry trees. This hands-on experience will be supplemented by support from Austin Osmanski, a dedicated project manager provided by the Harkess lab through the National Science Foundation CAREER award funding the American Campus Tree Genomes (ACTG) project. Dr. Osmanski will serve as a pseudo-TA, modifying existing course material to align with the project's needs and providing approximately 40 total hours of instructional support.
The intern's role will also extend to the educational and outreach components of the project. They will help develop materials such as flyers, billboards, and presentations to communicate the findings of the Yoshino Sequencing Project to the public. These outreach efforts will be particularly focused on the annual cherry blossom event, where the intern will assist in delivering presentations and engaging with visitors. This aspect of the role will provide the intern with valuable experience in science communication and public engagement, enhancing their overall educational experience. The student will work directly with contacts already established by Prof. Steinbrenner, including volunteers at the Brockman Campus Tree Tour, Courtney Coster of the UW Visitor Center and Sara Shores of the UW Campus Grounds team to coordinate these efforts.
Through their involvement in the Yoshino Sequencing Project, the student intern will gain comprehensive training in genomic research, from sample collection and DNA isolation to data analysis and public outreach. This multidisciplinary experience will not only contribute to the success of the project but also equip the intern with a diverse skill set applicable to their future scientific endeavors.