Matthew R. Thornton, BSc MSc

I joined the Plant Ecological Genomics group in 2020 to investigate the role of small RNA regulation for the ecology and evolution of a group of sibling allopolyploid marsh orchids (Dactylorhiza). Whole genome doubling is an ubiquitos and powerful process stimulating biodiversity and driving genome evolution. The formation of a allopolyploid is however a shock, as two divergent entire genomes are squashed together in a single nucleus, with important implications for the meiotic behaviour, the relationship between gene expression and the phenotype, the control of transposable elements, etc.

In my project, I focus of two diploid species (D. fuchsii, D. incarnata) and two of their allopolyploid offspring (D. majalis, D. traunsteineri) in hopes to better understand the molecular mechanisms associated with their origin. The two independently-formed allopolyploids share the same parental species, and they likely formed tens of thousand of generations ago, with D. traunsteineri being younger than its sibling. Despite their similar ancestry, they have divergent ecological preference, especially with regard to soil chemistry, and they are also morphologically distinct. I focus on smRNAseq data from common garden and reciprocal transplantation experiments to explore post-transcriptional regulation of the activity of ecologically important genes. Using reciprocal transplants I investigate the amount of plasticity in smRNA expression and how this may counteract gene flow between the specific environments of the two species. In addition, by comparisons to their diploid parents, we infer dominance and transgressive patterns in the sibling polyploids to understand the trans acting regulation of gene expression. Finally, we also address how small RNAs are involved in controlling the activity of transposable elements in the early stages after whole genome doubling. Given the ubiquity of polyploidization events in natural history it is fascinating to dig into how polyploid organisms, starting with similar genetic material, continue to differentiate through a variety of genetic and regulatory pathways.

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