Assembling and Mining the Genomes of Giant Antarctic Foraminifera

南极巨型有孔虫基因组的组装和挖掘

• 批准号: 1341612
• 负责人: Samuel Bowser
• 金额: $ 55万
• 依托单位: Health Research Incorporated/New York State Department of Health
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2019-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1341612&HistoricalAwards=false
• 关键词: Assembling; Mining; Genomes; Giant; Antarctic

Agglutinated foraminifera (forams for short) are early-evolving, single-celled organisms. These "living fossils" construct protective shells using sediment grains held together by adhesive substances that they secrete. During shell construction, agglutinated forams display amazing properties of selection - for example, some species build their shells of clear quartz grains, while other species use only grains of a specific size. Understanding how these single cells assemble complex structures may contribute to nanotechnology by enabling people to use forams as "cellular machines" to aid in the construction of nano-devices. This project will analyze the genomes of at least six key foram species, and then "mine" these genomes for technologically useful products and processes. The project will focus initially on the adhesive materials forams secrete, which may have wide application in biomedicine and biotechnology. Furthermore, the work will further develop a molecular toolkit which could open up new avenues of research on the physiology, ecology, and population dynamics of this important group of Antarctic organisms. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. Educational experiences related to the "thrill of scientific exploration and discovery" for students and the general public will be provided through freely-available short films and a traveling art/science exhibition. The project will also provide hands-on research opportunities for undergraduate students.Explorers Cove, situated on the western shore of McMurdo Sound, harbors a unique population of foraminiferan taxa at depths accessible by scuba diving that otherwise are primarily found in the deep sea. The project will use next-generation DNA sequencing and microdissection methods to obtain and analyze nuclear and mitochondrial genomes from crown members of two species each from three distinct, early-evolving foraminiferal groups. It will also use next generation sequencing methods to characterize the in-situ prokaryotic assemblages (microbiomes) of one of these groups and compare them to reference sediment microbiomes. The phyogenomic studies of the targeted Antarctic genera will help fill significant gaps in our current understanding of early foram evolution. Furthermore, comparative genomic analyses of these six species are expected to yield a better understanding of the physiology of single-chambered agglutinated forams, especially the bioadhesive proteins and regulatory factors involved in shell composition and morphogenesis. Additionally, the molecular basis of cold adaptation in forams will be examined, particularly with respect to key proteins.

凝集有孔虫（简称有孔虫）是早期进化的单细胞生物。这些“活化石”利用沉积物颗粒通过它们分泌的粘附物质结合在一起来构建保护壳。在壳的建造过程中，凝集有孔虫显示出惊人的选择特性-例如，一些物种用透明的石英颗粒建造它们的壳，而另一些物种只使用特定大小的颗粒。了解这些单细胞如何组装复杂的结构可能有助于纳米技术，使人们能够使用有孔虫作为“细胞机器”，以帮助构建纳米器件。该项目将分析至少六种关键有孔虫物种的基因组，然后“挖掘”这些基因组，以获得技术上有用的产品和工艺。该项目将首先关注有孔虫分泌的粘附材料，这可能在生物医学和生物技术中有广泛的应用。此外，这项工作还将进一步开发一个分子工具包，为这一重要南极生物群体的生理学、生态学和种群动态研究开辟新的途径。该项目还将进一步推动NSF的目标，即向公众提供科学发现和培训新一代科学家。将通过免费提供的短片和巡回艺术/科学展览，为学生和公众提供与“科学探索和发现的刺激”有关的教育经验。该项目还将为本科生提供动手研究的机会。探险家湾位于麦克默多湾的西海岸，拥有一个独特的有孔虫类群种群，其深度可通过水肺潜水到达，否则主要在深海中发现。该项目将使用下一代DNA测序和显微切割方法，从三个不同的早期进化有孔虫群体的两个物种的冠成员中获得和分析核和线粒体基因组。它还将使用下一代测序方法来确定其中一个群体的原核生物组合（微生物组）的特征，并将其与参考沉积物微生物组进行比较。南极目标属的植物基因组学研究将有助于填补我们目前对早期有孔虫进化的认识中的重大空白。此外，这六个物种的比较基因组分析预计会产生更好的了解单室凝集有孔虫的生理，特别是生物粘附蛋白和调控因子参与壳的组成和形态发生。此外，有孔虫冷适应的分子基础将被检查，特别是关于关键蛋白质。