Pan-genome variation and local adaptation in grasses

由于气候变化，地球上的生命正面临前所未有的挑战。了解生物如何快速适应环境不仅对减少即将灭绝的物种数量至关重要，而且对保障未来的粮食生产也至关重要。适应需要自然选择作用的遗传变异。我的研究将集中在基因存在和不存在的变异是如何产生的，以及最终如何影响适应。在同一细菌物种中，对多个个体的全套遗传指令进行比较的研究表明，有些基因存在于每个人身上，而另一些基因只存在于少数个体中。这导致了“泛基因组”的概念，即整个物种中存在的全部基因。最近的研究表明，动物和植物也有泛基因组，一个物种中的数千个基因具有可变的分布。基因含量的这种变化预计会对适应产生影响，特别是在物种范围的极端情况下。 高达60%的细菌泛基因组是通过横向基因转移（LGT）获得的，这是一个基因在物种之间转移而不繁殖的过程。这一过程也发生在植物和动物身上，尽管我们仍然不知道这一过程的全部进化含义。我的研究将集中在草家族，因为草包括所有已知的动物和植物LGTs中一些最令人信服的例子。我将使用DNA测序数据来生成几个草种的泛基因组，量化不同物种范围内不同种群的LGT变异，并测试这种变异是否与环境差异相关。我还将对这些植物进行基因操作，以实验验证我的发现。生物体还可以通过产生环状DNA分子来重新排列它们的基因组以应对环境压力，这使得它们能够增加它们所拥有的基因的拷贝数，以制造更多它们生存所需的蛋白质。我将对来自五种草的地理范围内的数百个个体的这些环状分子进行测序，以确定与eccDNA相关的基因内容的变化是否具有适应性意义。本人亦将测试该等移动的圆形元素是否作为草地对草地LGT的向量。如果eccDNA被确定为LGT背后的机制，它可能会从根本上改变我们对植物进化的看法。总的来说，这个项目将确定基因内容的变化是如何产生的，以及它对草的进化影响是什么，草是一个覆盖地球陆地表面30-40%的关键植物群，是我们大部分食物的来源。该项目也有可能从根本上改变我们对进化的理解，它也可能带来实际利益，包括设计抗气候变化的作物。

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.