Modeling plant adaptation in the context of climate change using genomics and epigenomics of stress tolerant Mangrove trees

Research Project

Project/Area Number	23K11509
Research Category	Grant-in-Aid for Scientific Research (C)
Allocation Type	Multi-year Fund
Section	一般
Review Section	Basic Section 64040:Social-ecological systems-related
Research Institution	Okinawa Institute of Science and Technology Graduate University
Principal Investigator	MIRYEGANEH Matin 沖縄科学技術大学院大学, 統合群集生態学ユニット, スタッフサイエンティスト (90793505)
Project Period (FY)	2023-04-01 – 2026-03-31
Project Status	Granted (Fiscal Year 2023)
Budget Amount *help	¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000) Fiscal Year 2025: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000) Fiscal Year 2024: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000) Fiscal Year 2023: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords	Mangroves / epigenetics / genomic / climate change
Outline of Research at the Start	This research uses stress tolerant mangrove trees as experimental model to study the role of epigenetic changes in responses to environmental stresses that are predicted by climate change. This proposed research will pair ecological methods in natural environments with genomic and epigenomic approaches in laboratories to provide comprehensive understandings of gene functions and adaptations of plants under stress. Additionally, it investigates whether and how epigenetic modification of the genome allow plants to respond to environmental stress.
Outline of Annual Research Achievements	Since the beginning of my Kakenhi project (Apr. 2023) I have successfully extracted the DNA from 2 other mangrove species (Rhizopphora stylosa, Kandelia obovata) and sequenced the genome, using PacBio-Hifi long read sequencing. I then de-novo assembled and annotated the genome. As for Hi-C sequencing, the 3 species of mangroves (Bruguiera gymnorhiza, Rhizopphora stylosa, Kandelia obovata) are being processed and library preparation is under preparation. These annotated genomes are the prerequisite of the downstream epigenetic analyses. In order to study the epigenetic stress memory, I have also done the DNA extraction and whole genome EM-seq sequencing for 96 samples (48 from Bruguiera gymnorhiza) and (48 from kandelia obovata). I have analyzed the data for the 48 samples from B. gymnorhiza and the results are very exciting. I also have extracted the RNA from the same samples and have sequenced them.
Current Status of Research Progress	Current Status of Research Progress 2: Research has progressed on the whole more than it was originally planned. Reason Everything is going as planned.
Strategy for Future Research Activity	Next I will analyze the data to investigate the association between expression of the genes and methylated regions of DNA.