Pan-genome variation and local adaptation in grasses

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Life on Earth is facing unprecedented challenges as a result of climate change. Understanding how organisms rapidly adapt to their environment is essential in not only reducing the number of species that will go extinct, but also in safeguarding future food production. Adaptation requires genetic variation for natural selection to act on. My research will focus on how variation in the presence and absence of genes is generated, and ultimately how this impacts adaptation. Research comparing the full set of genetic instructions in multiple individuals within the same bacterial species showed that some genes are present in everyone, whilst others are only found in a few individuals. This led to the concept of the 'pan-genome', the entire complement of genes present in a species as a whole. Recent work has shown that animal and plants also have pan-genomes, with thousands of genes within a species having a variable distribution. This variation in gene content is predicted to have consequences for adaptation, particularly at the extremes of a species range. Up to 60% of the bacterial pan-genome is acquired through lateral gene transfer (LGT), a process by which genes are transferred between species without reproduction. This process also occurs in plants and animals, although we still do not know the full evolutionary implications of this. My research will focus on the grass family as grasses include some of the most convincing examples of all known animal and plant LGTs. I will use DNA sequencing data to generate pan-genomes for several grass species, quantify variation in LGT in different populations across the species range, and test whether this variation correlates with environmental differences. I will also genetically manipulate the plants to experimentally validate my findings. Organisms can also rearrange their genomes in response to environmental stress by generating circular DNA molecules which allow them to increase the number of copies of the genes they possess to make more of the proteins they need to survive. I will sequence these circular molecules from hundreds of individuals across the geographic range of five grass species to determine if the variation in gene content associated with eccDNA is of adaptive significance. I will also test whether these mobile circular elements are acting as the vector of grass-to-grass LGT. If eccDNA is identified as the mechanism behind LGT, it may fundamentally change the way we view plant evolution.Overall, this project will determine how variation in gene content is generated and what its evolutionary impacts are for grasses, a key group of plants that cover 30-40% of the Earth's terrestrial surface and produce a majority of our food. This project also has the potential to fundamentally alter our understanding of evolution, and it may also lead to practical benefits including the design of climate change resistant crops.