Molecular and genome biology of dinoflagellate protists

鞭毛藻是一种单细胞微生物，在水生生境中具有重要的生态作用。除了作为初级生产者和营养物质回收者的作用外，它们还参与全球范围的现象，如有毒藻华（如赤潮）、形成珊瑚礁的珊瑚共生以及甲壳类动物和鱼类疾病。鞭毛藻的生物学在许多方面都是非凡的。也许在文献中发现的最显著的方面是它们极其巨大的基因组大小，在某些物种中可以达到人类基因组的100倍，以及它们细胞核的神秘性质，在某些方面与标准真核生物的细胞核非常不同。目前尚不清楚这些特性是如何产生和演变的。这个研究计划是解决的方面的谜生物学鞭毛藻。为此，我们正在进行世界性鞭毛藻Oxyrrhis marina的基因组测序。有了这些信息，我们将进行移动遗传元件（又名转座元件）跨几种鞭毛藻的一个全面的分析。这些元素是具有复制和“跳跃”到基因组其他部分能力的DNA片段。这些元素存在于包括动物和植物在内的许多生物中，并且可以通过它们的活动影响基因功能并引起进化变化。我们发现鞭毛藻基因组中富含某些类型的可移动元件，我们假设它们可以帮助解释鞭毛藻基因组的大尺寸。我们的分析将揭示移动元素影响基因组功能和进化的方式和程度。除了移动元素，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相关联而形成3D结构的方式。这种DNA和蛋白质的高度结构化混合物，即染色质，在鞭毛藻中有着显著的不同，但其细节却鲜为人知。我们将详细研究鞭毛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如何相互作用，以及这如何决定anc控制细胞分裂和基因表达等基本过程。该项目的完成将在各个层面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方面的领导地位。海洋微生物研究的进展与海洋研究相一致，海洋研究是我所在机构、新斯科舍省和联邦政府的首要任务之一。最后，本提案所涉及的工作包括在生物信息学、基因组学和分子生物学的前沿研究方面提供充足的基础和高级培训机会，为工业界和学术界提供更强大、高技能的劳动力。

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.