Comparative phylogenomics of lateral gene transfers among grasses

自然选择作用于物种内个体之间存在的遗传变异，是进化的主要驱动力。在动物和植物等多细胞生物中，直到最近，新的遗传变异都被认为是通过遗传物质从父母传给后代的随机突变而产生的。然而，近年来已经看到了不同的多细胞物种之间的基因转移在一个过程称为横向基因转移（LGT）的积累。LGT可以在遥远的谱系中传播适应性性状的功能基因，并且在植物中，它促进了低光照环境的定植，提高了高温下光合作用的效率，以及在不同土壤类型上茁壮成长的能力。因此，LGT可以导致巨大的进化飞跃，使植物能够迅速进化，超越其固有的潜力。然而，LGT的高频率也表明遗传物质可能从转基因作物中“逃逸”并转移到野生物种中。这可能会导致超级杂草的出现，从而降低作物产量并破坏自然生态系统。由于以往的研究缺乏专门的努力和稀疏的物种采样，LGT的进化重要性和频率在很大程度上仍然未知。在本项目中，我们将通过量化不同类群的LGT现象，并建立促进这种基因转移的因素，来确定LGT对植物进化的重要性。首先，我们将扫描大量开花植物的基因组，捕捉该群体的多样性，以检验一些植物谱系比其他植物谱系更容易交换基因的假设。其次，我们将分析一些开花植物中最重要的类群——草的多个个体的LGT。根据LGT在每个物种内个体之间的分布，我们的创新方法将独立于随后的损失率计算LGT的增益率。这将使我们能够检验这样一个假设：在所有物种中，随机获得LGT的比率都很高，但随后的损失率因选择制度的不同而不同。第三，我们将分析不同禾草物种捐赠LGT数量的变化，以确定作为转移来源的概率是否取决于物种的进化史、形态特征或地理起源。我们的多维项目将提供一个精确的量化的LGT的数量随着时间的推移，不同的植物群体获得和损失。此外，我们的创新方法将确定增加基因转移给远亲的可能性的因素。这一基础知识对于确定物种间基因交换对植物生态和功能多样化的重要性至关重要，可能导致对多细胞生物进化的生命之树性质的重新评估。此外，确定促进草地LGT的因素将有助于估计转基因作物基因逃逸的风险并制定缓解策略。

Natural selection acting on the genetic variation existing among individuals within a species is a major driving force in evolution. In multicellular organisms, such as animals and plants, novel genetic variants were assumed until recently to exclusively arise through random mutations in the genetic material passed from parents to offsprings. However, recent years have seen the accumulation of reports of gene transfers between distinct multicellular species in a process called lateral gene transfer (LGT). LGT can spread functional genes for adaptive traits among distant lineages, and in plants, it has facilitated the colonisation of low-light environments, improved efficiency of photosynthesis in high temperatures, and the ability to thrive on different soil types. LGT can therefore lead to big evolutionary leaps, allowing plants to rapidly evolve beyond their inherent potential. However, a high frequency of LGT would also suggest that genetic material might 'escape' from GM crops and be transferred to wild species. This could lead to the emergence of superweeds that would decrease crop yields and damage natural ecosystems. The evolutionary importance and frequency of LGT remain largely unknown due to a lack of dedicated efforts and sparse species sampling in previous studies. In this project, we will establish the importance of LGT for plant evolution by quantifying the phenomenon in various groups and establishing the factors that promote such gene transfers. Firstly, we will scan the genomes of numerous flowering plants capturing the diversity of the group to test the hypothesis that some lineages of plants are more likely to exchange genes than others. Secondly, we will analyse the LGT in multiple individuals of some grass species, the most important group of flowering plants ecologically and economically. From the distribution of LGT among individuals within each species our innovative approach will calculate the rates of gains of LGT independently from the rates of subsequent losses. This will allow us to test the hypothesis that the rate of random LGT gains is high in all species, but that the rate of subsequent losses varies because of different selection regimes. Thirdly, we will analyse the variation in the number of LGT donated by diverse grass species to determine whether the probability of being the source of the transfers depends on the evolutionary history, morphological characters or the geographic origin of the species. Our multidimensional project will provide a precise quantification of the amount of LGT gained and lost through time by diverse groups of plants. In addition, our innovative approach will establish the factors that increase the probability of transferring genes to distant relatives. This fundamental knowledge will be pivotal in establishing the importance of genetic exchanges between species on the ecological and functional diversification of plants, potentially leading to a reappraisal of the tree-of-life nature of evolution in multicellular organisms. In addition, the identification of the factors that promote LGT among grasses will help estimate the risk of gene escape from GM crops and develop mitigating strategies.