What role do epigenetics play in the adaptive capacity of a pioneer boreal tree? Birches are fast growing and widespread, experiencing considerable variation across the European distribution range including in temperature extremes and day lengths. Yet, birch pollen can travel many hundreds of kilometers, such that the population structure of silver birch is mostly very weak across its distribution range, limiting opportunities for local adaptation based on genetic variation. Do epigenetic mechanisms therefore help birches adapt to the environmental variation across the range? We are characterising epigenomic variation in the silver birch genome, studying its relationship to environmental and genetic variation (including heritability) and to phenotypic traits. For this we employ Epigenome-wide association (EWAS) mapping, controlled stress experiments and interrogation of population epigenomic variation across the European distribution range. The project receives funding from the Research Council of Finland.
Genomic structural variants (SVs) such as INDELs and inversions may be major contributors to epigenomic variation, as well as mediating local adaptation themselves. However, profiling structural variation in natural populations is challenging, especially with conventional short read sequencing which usually produces reads too short to capture large SVs. By assembling genomes from multiple representatives of silver birch from across the species range, we aim to construct a pangenome which collects common SVs and incorporates them into a unified reference that is more representative than a single linear reference genome. Doing so will allow us to more easily profile SV in natural populations, in turn allowing us to address how this SV shapes the epigenome and potentially plasticity. This project is in collaboration with the BMBG Group (Centre for Excellence in Tree Biology), receiving funding from the Research Council of Finland and the European Forest Institute.
The two species of tree birch that grow naturally in Europe: silver birch (Betula pendula) and downy birch (Betula pubescens) may look very much alike, but looks can be deceiving. The downy birch has a genome twice as large thanks to a recent whole genome duplication (WGD). The impact of WGD on epigenome dynamics is still not well understood, particularly in trees. Does having extra gene copies allow greater plasticity of the epigenome? In this project we combine comparative (epi)genomics, population studies and experimental approaches to test whether a tetraploid genome enhances the adaptability of birch via heightened epigenome flexibility. This project is in collaboration with the BMBG group, and receives funding from the University of Helsinki (Doctoral scholarship for Yulin Zheng) and the Research Council of Finland.
Stochastic variation in DNA methylation is an overlooked, but potentially important source of adaptive variation. What factors drive the methylome to have more, or less stochastic variation? Under which conditions are heightened stochasticity potentially adaptive? We address these questions using data from a diverse taxa.
We strive to be at the forefront of applications of machine learning in biology. In collaboration with the Department of Computer Science and the Vaten Lab (OEB), we have worked to develop a machine learning tool for automated phenotyping of birch leaf microscopy images, specifically to measure the size and number of stomatal pores.