Excellence in Research: Genome Evolution of Amoebozoa: Resolving the deep phylogeny of Amoebozoa through genomic and proteomic features.

微生物在我们对许多细胞过程的理解中发挥了重要作用。它们构成了所有生物体的大多数，但人们对它们的多样性、行为和基因组学知之甚少。这个项目的重点是属于阿米巴虫超群的变形虫生物。它们存在于不同的自然栖息地，包括海洋、淡水和土壤环境，并作为影响牲畜和人类的共生体或寄生虫存在。阿米巴虫一直被认为是简单和原始的，但最近的研究表明，它们比以前认为的要复杂得多。尽管变形虫具有重要的进化和生态意义，但其生物多样性和进化尚不清楚。该项目结合了包括全基因组分析和先进显微镜在内的方法来解决它们的系统发育（它们彼此之间的关系）。该项目还将研究关键的进化特征，如基因组大小和复杂性，以及变形虫运动的机制。关于变形虫运动的知识在变形虫之外具有广泛的意义。它将为使用类似运动机制的群体提供见解，例如包括巨噬细胞和癌细胞在内的哺乳动物细胞。该项目还将为非洲裔美国妇女和高级显微镜学、基因组学、蛋白质组学、系统基因组学和微生物多样性方面的博士后提供跨学科培训。近年来的分子研究使我们对变形虫的多样性和进化的认识取得了重大进展。然而，阿米巴原虫亚群之间的深层关系在很大程度上没有得到解决，一些关键的谱系在阿米巴原虫树中仍然没有找到。超级类群阿米巴虫是一个古老的谱系，据估计是在10亿年前从一个共同的祖先进化而来的。由于数据有限以及其他历史和算法方面的挑战，解决古代关系是一项艰巨的任务。该项目将使用包括细胞蛋白质组学和全基因组测序在内的多种方法来解决变形虫树的问题。基因组测序不仅将提供大量有助于解决阿米巴虫树的遗传数据，而且还将提供额外的基因组结构数据，可用于研究该群体的进化。鉴于阿米巴虫在生命之树中占有关键的进化地位，解决阿米巴虫之树将阐明许多基本的进化问题，包括生命周期的起源和进化、多细胞性、宿主-寄生虫相互作用、阿米巴虫运动和跨域水平基因转移（HGT）。除此之外，对阿米巴原虫基因组及其复杂性的研究将有助于了解基因组大小如何影响行为和适应各种生态位。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Microscopic organisms have played an instrumental role in our understanding of many cellular processes. They constitute the majority of all living organisms, yet little is known about their diversity, behavior and genomics. This project focuses on amoeboid organisms belonging to the supergroup Amoebozoa. They exist in diverse natural habitats including marine, freshwater, and soil environments, and as symbionts or parasites affecting livestock and humans. Amoebozoans have long been considered simple and primitive, but recent studies have shown that they are more complex than previously thought. Despite their evolutionary and ecological significance, the biodiversity and evolution of Amoebozoans is not well understood. This project uses a combination of methods including whole genome analysis and advanced microscopy to resolve their phylogeny (how they are related to each other). The project will also examine key evolutionary features such as genome size and complexity as well as mechanisms of amoeboid movement. Knowledge of amoeboid movement has broad implications beyond Amoebozoans. It will give insights into groups that employ similar locomotive mechanisms, such as mammalian cells including macrophages and cancer cells. This project will also provide interdisciplinary training for women of African American origin and a postdoctoral fellow in advanced microscopy, genomics, proteomics, phylogenomics and microbial diversity.Recent molecular studies made significant progress in our understanding of Amoebozoan diversity and evolution. However, the deep relationships among Amoebozoan subgroups are largely unresolved and some key lineages remain unplaced in the tree of Amoebozoa. The supergroup Amoebozoa is an old lineage, estimated to have evolved from a common ancestor over a billion years ago. Resolving ancient relationships is a difficult endeavor due to limited data and other historic and algorithmic challenges. This project will use a combination of approaches including cellular proteomic and whole genome sequencing to resolve the tree of Amoebozoa. Genome sequencing will provide not only large amounts of genetic data helpful for resolving the tree of Amoebozoa but also additional genomic architectural data that can be used to study the evolution of the group. Given that Amoebozoa holds a key evolutionary position in the tree of life, resolving the tree of Amoebozoa will elucidate many fundamental evolutionary questions including the origin and evolution of life cycles, multicellularity, host-parasite interactions, amoeboid movement, and horizontal gene transfer (HGT) across domains. In addition to this, study of Amoebozoan genomes and their complexity will give insights on how genome size impacts behavior and adaptation to various ecological niches.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.