Using green algae to unravel the origins of genome architecture

来自整个生命树的遗传序列数据揭示了基因组结构的巨大变异，但导致这种变异的力量却鲜为人知。在生物界最多样和最古怪的基因组中，微生物真核生物(原生生物)是其中之一。在过去的五年里，我对真核生物和原生生物基因组进化的研究做出了重大贡献，发表了21篇同行评议的文章，并就这一主题发表了10次会议演讲和应邀研讨会。 在接下来的五年里，我提出的研究计划将重点放在含叶绿体的原生生物(藻类)上，重点是绿藻，包括具有医疗和工业重要性的物种，以及失去光合作用能力的类群。使用生物信息学和湿实验室技术，我们将描述关键绿藻谱系中的“极端”基因组，探索拥有这些基因组的种群内部和种群之间潜在的遗传多样性，并使用这些数据来检验当代假说和开发关于基因组进化的新理论。 这项拟议工作的主要主题是：非适应性力量与适应性力量如何影响基因组的大小和结构？通过利用藻类在进化中的主要转变(例如，单细胞与多细胞；无性与有性；光合作用与非光合作用；自由生活与寄生)，我们希望了解基因组结构和遗传多样性是如何与更广泛的生命特征联系在一起的。例如：失去光合作用能力的基因组后果是什么？而且，基因组结构的非适应性变化是否为导致多细胞的适应性进化类型提供了模板？鉴于藻类对工业和环境的重要性，以及基因组结构与遗传信息的遗传和表达方式之间的密切联系，该研究计划的结果可能会对生命科学中的许多学科产生广泛的影响。这项工作还将帮助培训和发展大约5名研究生和15名本科生。

Genetic sequence data from across the tree of life have revealed a huge variation in genome architecture, but the forces responsible for this variation are poorly understood. Among the most diverse and eccentric genomes in the biological world belong to microbial eukaryotes (protists). In the past five years, I have made significant contributions to the study of eukaryotic and protist genome evolution, publishing 21 peer-reviewed articles and giving 10 conference presentations and invited seminars on the subject. Over the next five years, my proposed research program will focus on plastid-containing protists (algae), with emphasis on green algae, including species of medical and industrial importance, and taxa that have lost photosynthetic capabilities. Using bioinformatic and wet-lab techniques, we will characterize "extreme" genomes within key green algal lineages, explore the underlying genetic diversity within and between the populations that harbour these genomes, and use these data to test contemporary hypotheses and develop new theories on genome evolution. The overarching theme of the proposed work is: How do non-adaptive vs adaptive forces influence genome size and structure? By employing algae that span major transitions in evolution (e.g., unicellular vs multicellular; asexual vs sexual; photosynthetic vs non-photosynthetic; free-living vs parasitic), we hope to understand how genome architecture and genetic diversity are linked to broader life traits. For instance: What are the genomic consequences of losing photosynthetic capabilities? And, do non-adaptive changes to genome structure provide the template for the types of adaptive evolution that can lead to multicellularity? Given the importance of algae to industry and the environment, and the intimate connection between genome structure and how genetic information is inherited and expressed, the results from this research program could have wide-reaching implications for many disciplines within the life sciences. This work will also help in the training and development of approximately five graduate and fifteen undergraduate students.