Lead supervisor: Ian Henderson, Plant Sciences
Co-supervisor: Adam Pellegrini, Plant Sciences
Brief summary:
As English Oak (Quercus robur) trees can live for >1,000 years, there is a high potential for the genome and epigenome to evolve along branches - this project will use long-read DNA sequencing to map genome evolution within ancient oak trees and relate this to ecological adaptation.
Importance of the area of research concerned:
English Oak (Quercus robur) can live for >1,000 years and must continue to adapt over periods of considerable climate change. During tree development, there is a high potential for the genome, and epigenome, to evolve along the branches. However, the rates of genome evolution within ancient trees, how this is influenced by the environment, and the relevance for ecological adaptation remain unclear. As seed (acorns) form de novo on tree branches, there is also a high potential for transmission of new genetic and epigenetic variants to the next generation. This means individual trees have the potential to produce genetically distinct progeny as a consequence of intra-individual divergence. Therefore, measuring genome evolution within ancient trees is vital to understand their biology, diversity and will additionally inform how to conserve and maintain them. As ancient trees can experience significant change to ecological change over their life-span, this work will reveal how intra-individual genetic and epigenetic diversification facilitates continued adaptation to the changing environment and climate.
Project summary :
We will collect material from multiple branches of ancient oak trees, from a variety of ecological settings in the UK, including open parkland and within woods, and relevant ecological meta-data collected from each site. We will extract high molecular weight DNA from multiple branches of each tree and generate Nanopore sequencing libraries. Sequencing data will be analysed to quantify patterns of genome evolution across the branches. Nanopore sequencing will be used in parallel to derive maps of DNA methylation, allowing epigenetic divergence along the branches to be analysed. The project will test the hypothesis that trees located on the edge of the ecological range will show greater rates of somatic genome evolution. To investigate the transgenerational significance of genome change, acorns will be collected from selected branches and tested for physiological phenotypes.
What will the student do?:
The student will select multiple ancient Q. robur trees from across the UK in diverse ecological settings. They will sample leaf material from multiple branches, extract genomic DNA and perform long read sequencing. Using these sequence data, they will assemble the genomes, and profile DNA methylation, along the branches of individual trees. The genomes will then be analysed for gene and repeat structure and mutational patterns, which will further be analysed by the student using population genetics. These data will be publicly released for reuse by the community. The student will analyse patterns of genome evolution, within and between trees, and relate this to their ecological context and adaptation. The student will collect acorns from selected branches that show genetic and/or epigenetic divergence, and physiological analysis performed on the resulting seedlings. They will vary temperature and water availability in these experiments to investigate environmental adaptation. The student will also develop resources that communicate information on tree longevity and genome evolution to the public, via science festivals or partnering with educational institutions or charities.
References - references should provide further reading about the project:
Hofmeister BT, Denkena J, Colomé-Tatché M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Jacobsen D, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ. (2020) A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol. 2020 21:259 doi:10.1186/s13059-020-02162-5.
This study provides a model for analysis of genetic and epigenetic change within Poplar trees.
Wlodzimierz P, Rabanal FA, Burns R, Naish M, Primetis E, Scott A, Mandáková T, Gorringe N, Tock AJ, Holland D, Fritschi K, Habring A, Lanz C, Patel C, Schlegel T, Collenberg M, Mielke M, Nordborg M, Roux F, Shirsekar G, Alonso-Blanco C, Lysak MA, Novikova PY, Bousios A, Weigel D, Henderson IR. (2023) Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature. 2023 618:557-565 doi:10.1038/s41586-023-06062-z.
This study uses long-read sequencing in the model plant Arabidopsis thaliana to explore rapid evolution of the centromere regions. In this project similar approaches will be taken within ancient oak trees.
Christophe Plomion, et al Jérôme Salse (2018) Oak genome reveals facets of long lifespan. Nature Plants 4, pages 440–452.
This study uses previous short-read sequencing data to analyse the oak genome. This project will extend this approach by harnessing long-read sequencing to assemble complete oak genomes.
Applying
You can find out about applying for this project on the Department of Plant Sciences page.