Assembling and Mining the Genomes of Giant Antarctic Foraminifera

凝集有孔虫(简称有孔虫)是早期进化的单细胞生物体。这些“活化石”使用沉积物颗粒构建保护壳，沉积物颗粒由它们分泌的粘性物质结合在一起。在建造贝壳的过程中，粘合的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贝壳，而另一些物种只使用特定大小的颗粒。了解这些单个细胞如何组装复杂的结构可能有助于纳米技术，因为它使人们能够将孔洞用作“细胞机器”来帮助构建纳米设备。该项目将分析至少六个关键有孔虫物种的基因组，然后从这些基因组中“挖掘”出技术上有用的产品和工艺。该项目首先将重点放在孔洞分泌的粘连材料上，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箱，为研究这一重要的南极生物群体的生理、生态和种群动力学开辟新的途径。该项目还将推动NSF向公众提供科学发现和培训新一代科学家的目标。将通过免费提供的短片和巡回艺术/科学展览，为学生和普通公众提供与“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。探索者湾位于麦克默多海峡的西岸，在潜水可到达的深处拥有独特的有孔虫分类群，否则主要在深海中发现。该项目将使用下一代DNA测序和显微解剖方法，从三个不同的早期进化有孔虫类群的两个物种的树冠成员中获取和分析核和线粒体基因组。它还将使用下一代测序方法来表征其中一组的原位原核生物组合(微生物群)，并将它们与参考沉积物微生物群进行比较。对目标南极属的系统发育研究将有助于填补我们目前对早期有孔虫演化的认识上的重大空白。此外，对这六个物种的比较基因组分析有望更好地了解单腔凝集有孔虫的生理，特别是涉及贝壳组成和形态发生的生物黏附蛋白和调节因子。此外，还将研究有孔虫冷适应的分子基础，特别是关于关键蛋白质的分子基础。

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.