Project highlights

  • We will test if trees have a molecular memory of past environmental stresses
  • We will apply most advanced DNA sequencing approaches to investigate woods
  • For the first time, we will explore relations between epigenetic and dendrochronology data in trees

Overview

Trees are long living, sessile organisms that represent a fundamental component of most of earth ecosystems. Being immobile during their life, trees need to efficiently adapt to changes of environment and to stresses, in order to reach maturity and reproduction. However, contrary to animals, trees do not rely on a learning strategy based on a central-nervous apparatus, and the existence of certain form of adaptive memory in these organisms is debated.

Recent advanced in genomics studies are always more convincingly showing that environmental information can be recorded at molecular level on DNA through epigenetic marks. Epigenetics studies molecular changes of DNA (mostly DNA methylation) in response to developmental or environmental stimuli, which does not involve a change of the DNA sequence itself. These changes can be inherited during cell division and are particular stable in plants, where they represent the base of an epigenetic “memory”, which remains encoded in biological tissues and can be transmitted to progenies.

In trees, wood is produced by plant cells that lignified and die to provide physical functions such as of mechanical support, storage and water conduction. However, part of their DNA is preserved unaltered, and retains the epigenetic information encoded in the cells in the moment they died. In temperate zones, most trees produce in their wood one growth-ring each year, so that the entire period of a tree’s life remain impressed in its wood material. As wood growth is affected by environmental conditions, trees have marks of past interactions with the environment recorded into their wood as they grow, at both physical and molecular level. However, while physical propriety of tree rings is well investigated, the possible epigenetic changes associated to the residual DNA in different rings re.

This project aims to understand how trees use environmental information to adapt to a changing condition. This will be done by extracting DNA from different parts of tree rings and compare their epigenetic profiles. The PhD researcher will compare the DNA methylation from different tree rings and associate epigenetic changes to historical and ecological record of drought. This will allow to connect tree molecular and physical responses to the environment in in tree rings, creating for the first time a direct connection among dendrochronology, ecology and epigenetic data in trees.

Host

University of Birmingham

Theme

  • Organisms and Ecosystems

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

The project will require to merge molecular, computational, and ecological methodologies. We will adapt newly developed protocols of DNA extraction from oak wood to produce libraries for high-throughput sequencing analysis, to generate genome-wide single cytosine resolution maps of DNA methylation of wood cells located in different portion of a tree ring sample.

Then, we will analyse tree-rings from oak samples located at the BIFoR facility (University of Birmingham), for which historical records of past drought stress are available. We will determined physical changes in wood associated to drought stress and we will determine the associated portion of epigenetic changes found in each ring portion.

Finally, we will compare and validate our result with analysis performed on oak seedling drought stressed in controlled condition (greenhouses), to determine a final set of DNA regions that can be used to track past event of water deprivation in oak wood.

Training and skills

The candidate would join the School of Biosciences and the School of Geography, Earth and Environmental Sciences where we have a vibrant community of researchers working on diverse plant species. Specifically, the student will be directly supervised by two PIs, and will benefit from peer-discussion occurring during weekly lab meeting sessions. We also have close connections with the Centre for Computation Biology, which provides further expertise in genomic analysis. Additionally, the student will have access to training programmes run by the University, these include training in bioinformatics and career development workshops for postgraduate students organised through our graduate school.

Partners and collaboration

The supervision of the project relies on the collaboration between academics with strong background in plant ecology (Dr Esquivel-Muelbert) and molecular biology/genomics (Dr. Catoni). In addition, the project is supported by Forest Research

Further details

If you wish to apply to the project please visit: https://sits.bham.ac.uk/lpages/LES068.htm

Possible timeline

Year 1

Based on a previous developed protocol of DNA extraction from wood, designed for high throughput sequencing, you will develop a procedure for BS-seq (bisulfite DNA treatment and sequencing) starting from oak tree rings. The student will produce and compare single cytosine methylation profiles from multiple replicates and we will optimise the computational pipeline to determine differentially methylated regions in Oak genome.

Year 2

You will collect different tree rings from oaks from the BIFoR site, and collect and analysed ecological data of the area. The method established in year 1 will be then used to produce the DNA methylation profiles of different tree rings (ideally, a sequenced library collected at 4-5 regions per sample). Then you will use different epigenetic analysis (clustering, PCA) to determine the variability across replicates and significant epigenetic differences which are specific of certain tree ring areas.

Year 3

You will integrate precipitation over the last 50 years at the BIFoR site with the variation in the epigenetic profile observed in wood area formed at different years, and will determine a core of chromosomal areas that can store molecular memory of drought stress in trees.

Further reading

Zeng, Z., Raffaello, T., Liu, M.-X., and Asiegbu, F.O. (2018). Co-extraction of genomic DNA & total RNA from recalcitrant woody tissues for next-generation sequencing studies. Future Science OA 4, FSO309.

COVID-19

A consistent amount of this work will require computational analysis. Therefore, a possible lookdown will have little impact because this part can be done with a smart working arrangement. In addition, being the project co-supervised by two PIs, direct supervision will always be available also if one of the PI will become sick or will require isolation. If experimental work will not be possible at all in the three years of the project, then the work will focus in analysing epigenetic profiles already generated by the PIs as part of NERC-funded project (MEMBRA), using them to investigate epigenetic memory.