Molecular and genome biology of dinoflagellate protists

甲藻是一种单细胞微生物，因其在水生生境中的重要生态作用而臭名昭著。除了作为初级生产者和营养循环者的作用外，它们还参与全球范围的现象，如有毒藻华(例如赤潮)、形成珊瑚礁的珊瑚共生以及甲壳类和鱼类疾病。甲藻的生物学在许多方面都非同寻常。也许在文献中发现的最明显的方面是它们极大的基因组大小，在某些物种中可以达到人类基因组的100倍，以及它们的细胞核的神秘性质，在某些方面与标准的真核细胞核非常不同。目前还不清楚这些特殊性是如何起源和演变的。这项研究计划正在解决甲藻的神秘生物学方面的问题。为此，我们正在对世界各地的甲藻进行基因组测序。有了这些信息，我们将对几种甲藻的可移动遗传元件(也称为转座元件)进行全面分析。这些元素是DNA片段，具有复制和‘跳跃’到基因组其他部分的能力。这些元素存在于包括动物和植物在内的许多生物体中，并可以通过它们的活动影响基因功能并导致进化变化。我们发现甲藻基因组富含某些类型的可移动元素，我们假设它们可以帮助解释甲藻基因组的大小。我们的分析将揭示移动元素以什么方式以及在多大程度上影响基因组功能和进化。除了可移动的元素外，我们还将探索基因组和细胞核的其他方面。真核生物中最保守的特征之一是DNA通过与一种称为组蛋白的蛋白质结合而在3D结构中组织的方式。这种高度结构化的DNA和蛋白质混合物，称为染色质，在甲藻中有很大的不同，但细节鲜为人知。我们将详细研究甲藻中染色质和染色体的分子组织，以了解蛋白质和DNA在细胞周期的不同阶段是如何相互作用的，以及这如何决定ANC控制细胞分裂和基因表达等基本过程。该项目的建成将在各个层面上对加拿大产生积极影响。这将有助于加强加拿大在微生物真核生物基因组学和分子生物学领域的领先地位。海洋微生物研究的进展与海洋研究相一致，海洋研究是我的机构新斯科舍省和联邦政府的首要优先事项之一。最后，这项提议所涉及的工作包含了在生物信息学、基因组学和分子生物学的前沿研究方面进行基础和高级培训的大量机会，有助于培养一支更强大、技能更高的劳动力队伍，为工业界和学术界提供服务。

Dinoflagellates are single-celled microbes notorious for their important ecological roles in aquatic habitats. In addition to their roles as primary producers and nutrient recyclers, they are involved in phenomena of global scale such as toxic algal blooms (e.g. red tides), reef-forming coral symbioses and crustacean and fish diseases. The biology of dinoflagellates is extraordinary in many ways. Perhaps the most conspicuous aspects found in the literature is their extremely large genome size, which in certain species can reach a hundred times the human genome, and the enigmatic nature of their cell nucleus which is in some ways very different from the standard eukaryotic nucleus. It is still unclear how these particularities originated and evolved. This research program is addressing aspects of the enigmatic biology of dinoflagellates. For this, we are conducting genome sequencing of the cosmopolitan dinoflagellate Oxyrrhis marina. With this information we will conduct an encompassing analysis of mobile genetic elements (a.k.a transposable elements) across several species of dinoflagellates. These elements are pieces of DNA with the ability to replicate and `jump' to other parts of the genome. Such elements exist in many organisms including animals and plants and can, through their activity, affect gene function and cause evolutionary change. We found that dinoflagellate genomes are rich in certain types of mobile elements and we hypothesize that they could help explain the large genomes size in dinoflagellates. Our analysis will reveal in what ways and how much do mobile elements affect genome function and evolution. In addition to mobile elements we will be exploring other aspects of the genome and nucleus. One of the most conserved features among eukaryotes is the way in which DNA organizes in 3D structures by associating with a type of proteins known as histones. This highly structured mix of DNA and proteins, known as chromatin, is remarkably different in dinoflagellates but the details are poorly known. We will investigate in detail the molecular organization of chromatin and chromosomes in dinoflagellates looking to understand how proteins and DNA interact during the different phases of the cell cycle, and how this determines anc controls essential processes such as cell division and gene expression. Completion of this project will generate positive impact for Canada in various levels. It will help strengthen Canada's reputation of a leader in genomics and molecular biology of microbial eukaryotes. Advancement of research on marine microorganisms aligns with Ocean Research, one of the top priorities for my institution, Nova Scotia and the Federal Government. Finally, the work involved in this proposal contains ample opportunities for basic and advanced training in cutting edge research in bioinformatics, genomics and molecular biology, contributing to a stronger and highly skilled workforce that feed both industry and academia.