Collaborative Research: The Genomic Basis of Multicellularity and Developmental Complexity in the Volvocine Algae

合作研究：卷藻多细胞性和发育复杂性的基因组基础

• 批准号: 1412395
• 负责人: Richard Michod
• 金额: $ 27.9万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1412395&HistoricalAwards=false
• 关键词: Collaborative; Research; Genomic; Basis; Multicellularity

The visible organisms around us are composed of many microscopic cells. In contrast, it was only with the invention of the microscope that it was realized that organisms exist that are composed of a single cell. Thus, a fundamental question in biology has been to understand how microscopic unicellular organisms evolved the ability to cooperate as a group to form large and complex organisms composed of multiple cells (multicellular). In the most familiar organisms such as animals and plants, the transition from single cells to multicellular organisms occurred about a billion years ago in organisms that no longer exist, which has made it very challenging to identify the genes involved in this evolutionary process. However, in a group of organisms that live in ponds called the Volvocine algae, the transition from single cells to multicellular organisms occurred more recently resulting in the preservation of the genetic signature of multicellular evolution within their present day relatives. While Volvocine algae were once simply known as "pond scum", they are now known to be representative of simple forms of other organisms such as plants and animals, thus making them a valuable tool for understanding how multicellular plants and animals evolved. The Volvocine algae are now recognized as an important model for multicellular evolution, often appearing in science textbooks and are featured at the Smithsonian Museum as one of the primary examples of how multicellularity evolved. To determine which genes are important for multicellularity in the Volvocine algae, their genomes will be sequenced and compared to identify those genes that are evolving in multicellular algae compared to close relatives that are unicellular. Once identified, these genes will be independently tested to confirm that they are indeed important for the transition to multicellularity. Because the Volvocine algae are similar to other organisms, including plants and animals, the data generated in this project will be broadly important toward understanding how multicellular organisms evolved in all domains of life. During the course of this project there will be opportunities for local high school, undergraduate and other trainees to participate in this effort, including outreach to a high school where less than 20% of students have college-educated parents. The genome data generated from this project will become publicly available on the Phytozome website (http://www.phytozome.net), and this project will also contribute additional data about the Volvocine algae to an international education effort, the Volvocales Information Project (http://www2.unb.ca/vip/).The evolution of multicellularity is a major evolutionary transition that resulted in a fundamental change in cellular organization and function. However, the genetic basis of multicellularity is not well understood. Multicellular evolution involves three major evolutionary steps: first colonial multicellular organisms evolve when individual cells come together in a cooperative group; then cell fate determination evolves such that there are two distinct germ and somatic cell lines, finally organismal size expands and cells evolve specialized function. The goal of this project is to determine the underlying, and succinct genetic changes that are required for the evolution of colonial cooperative groups, the evolution of germ-soma, and the evolution or organismal size by using a comparative genomics approach. The project will utilize the Volvocine algae as a model system that has undergone the most recent example of multicellular evolution. The Volvocales are an excellent model system for multicellularity because member species show stepwise gains and losses of multicellular characters. The central hypothesis of this project is that existing genetic pathways in unicellular Chlamydomonas have been evolutionarily co-opted as complexity increased in the Volvocales. To test this hypothesis, the PI will (a) sequence and compare the contents of the genomes of Volvocales representative of the three major steps to multicellularity to identify candidate genes and pathways that have been co-opted into new functions correlating with multicellularity and organismal complexity, (b) use comparative differential expression analysis between species to identify genes whose expression pattern is altered and correlated with multicellularity in the Volvocales, and (c) functionally test candidate genes to see when in the Volvocales their function was co-opted by determining if they positively cause multicellularity by expressing them in unicellular Chlamydomonas and looking for morphological changes. This project will not only identify genes associated with the evolution from uni- to multicellularity, but also challenge the prevailing hypothesis in the field, which suggests that large-scale genomic duplication and neo-functionalization events underlie multicellularity. The project is a collaboration between two PIs, whose complimentary expertise is essential to achieve its stated goals. Another goal of the project is to promote participation of high school and undergraduate students from underrepresented groups and who are first generation college students. Both laboratories are located near rural areas that struggle with modernizing their high school science programs. High school participants in this project will be trained in two steps. First, the PIs will provide outreach to their high school collaborators to build in class units for teaching molecular genotyping of phylogenetic classification or organisms. Next, students will participate in weekend visits to KSU and U of Az where they use their in-class derived skills to PCR genotype algal strains that will be used for the population studies in the project. Students who have a strong interest in science will given the opportunity to be interns in the PI's laboratory during the summer. Student interns will travel to locations in the USA and assist with isolating new Volvocales strains for the population studies and then use their training to molecularly genotype the strains they have isolated. Importantly, the students will also determine the taxa present in the ponds, and sample the water for quality measurements, to build toward a future project.

我们周围可见的生物体是由许多微观细胞组成的。相比之下，直到显微镜的发明，人们才意识到生物体是由单个细胞组成的。因此，生物学的一个基本问题是了解微观单细胞生物如何进化出作为一个群体合作的能力，形成由多个细胞（多细胞）组成的大型复杂生物体。在我们最熟悉的生物体（如动物和植物）中，从单细胞生物到多细胞生物的转变发生在大约十亿年前，但现在已不复存在，这使得识别参与这一进化过程的基因变得非常具有挑战性。然而，在一群生活在池塘中的称为沃尔沃辛藻的生物体中，从单细胞生物到多细胞生物的转变是最近发生的，导致其当今的亲属中保留了多细胞进化的遗传特征。虽然沃尔沃辛藻曾经被简单地称为“池塘浮渣”，但现在人们知道它们代表了植物和动物等其他生物体的简单形式，从而使它们成为了解多细胞植物和动物如何进化的宝贵工具。沃尔沃辛藻现在被认为是多细胞进化的重要模型，经常出现在科学教科书中，并作为多细胞进化的主要例子之一在史密森博物馆展出。为了确定哪些基因对于沃尔沃辛藻类的多细胞性很重要，将对它们的基因组进行测序和比较，以识别那些在多细胞藻类中与单细胞近亲相比进化的基因。一旦确定，这些基因将被独立测试，以确认它们对于向多细胞的过渡确实很重要。由于沃尔沃辛藻类与包括植物和动物在内的其他生物体相似，因此该项目生成的数据对于了解多细胞生物体如何在生命的所有领域中进化具有广泛的重要意义。在该项目进行期间，当地高中、本科生和其他受训人员将有机会参与这项工作，包括向一所拥有受过大学教育的学生的高中进行推广。该项目生成的基因组数据将在 Phytozome 网站 (http://www.phytozome.net) 上公开，并且该项目还将为国际教育工作、Volocales 信息项目 (http://www2.unb.ca/vip/) 贡献有关Volvocine 藻类的额外数据。多细胞生物的进化是一个重大的进化转变，它导致了多细胞生物的进化。 细胞组织和功能发生根本性变化。然而，多细胞性的遗传基础尚不清楚。多细胞进化涉及三个主要的进化步骤：首先，当单个细胞聚集成一个合作群体时，群体多细胞生物就会进化；然后细胞命运决定进化，从而出现两种不同的生殖细胞和体细胞系，最后生物体尺寸扩大并且细胞进化出专门的功能。该项目的目标是通过使用比较基因组学方法来确定殖民合作群体的进化、生殖体的进化以及生物体大小的进化所需的潜在的、简洁的遗传变化。该项目将利用Volvocine藻类作为模型系统，该系统经历了多细胞进化的最新例子。团藻目是一个优秀的多细胞模型系统，因为成员物种表现出多细胞特征的逐步增强和丧失。该项目的中心假设是，随着团藻目复杂性的增加，单细胞衣藻中现有的遗传途径已被进化选择。为了检验这一假设，PI 将 (a) 对代表多细胞性三个主要步骤的团藻目基因组内容进行测序和比较，以识别已被纳入与多细胞性和生物体复杂性相关的新功能的候选基因和途径，(b) 使用物种之间的比较差异表达分析来识别表达模式发生改变并与多细胞性相关的基因。 (c) 对候选基因进行功能测试，通过在单细胞衣藻中表达候选基因并寻找形态变化来确定它们是否积极导致多细胞性，以了解它们的功能何时在团藻目中被增选。该项目不仅将鉴定与从单细胞向多细胞进化相关的基因，还将挑战该领域的普遍假设，即大规模基因组复制和新功能化事件是多细胞的基础。该项目是两名 PI 之间的合作，他们的互补专业知识对于实现其既定目标至关重要。该项目的另一个目标是促进代表性不足群体的高中生和本科生以及第一代大学生的参与。这两个实验室都位于农村地区附近，这些地区正在努力实现高中科学项目的现代化。该项目的高中参与者将分两步接受培训。首先，PI 将向他们的高中合作者提供外展服务，建立课堂单元来教授系统发育分类或生物体的分子基因分型。接下来，学生将参加周末参观肯尼迪州立大学和亚利桑那大学，在那里他们利用课堂上获得的技能对藻类菌株进行 PCR 基因分型，这些藻类菌株将用于该项目的种群研究。对科学有浓厚兴趣的学生将有机会在暑期到PI实验室实习。学生实习生将前往美国各地，协助分离新的藻类菌株以进行种群研究，然后利用他们的培训对他们分离的菌株进行分子基因分型。重要的是，学生们还将确定池塘中存在的类群，并对水进行采样以进行质量测量，以构建未来的项目。