Using green algae to unravel the origins of genome architecture

来自整个生命之树的基因序列数据揭示了基因组结构的巨大变化，但导致这种变化的力量却知之甚少。生物世界中最多样化和最古怪的基因组属于微生物真核生物（原生生物）。在过去的五年中，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篇同行评审的文章，并就该主题发表了10次会议演讲和邀请研讨会。在接下来的五年里，我提出的研究计划将集中在含有质体的原生生物（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分类群。利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，探索隐藏这些基因组的种群内部和种群之间的潜在遗传多样性，并使用这些数据来测试当代假设并发展基因组进化的新理论。提出的工作的首要主题是：非适应性和适应性力量如何影响基因组的大小和结构？通过使用跨越进化主要转变的藻类（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如何与更广泛的生命特征联系在一起。例如：失去光合作用能力的基因组后果是什么？基因组结构的非适应性变化是否为导致多细胞生物的适应性进化提供了模板？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如何遗传和表达之间的密切联系，这项研究计划的结果可能对生命科学的许多学科产生广泛的影响。这项工作还将有助于培训和发展大约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.