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

我们周围可见的有机体是由许多微小的细胞组成的。相反，直到发明了显微镜，人们才认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理解微观单细胞生物如何进化出作为一个群体合作的能力，形成由多个细胞组成的大型复杂生物（多细胞）。在动物和植物等最常见的生物中，从单细胞到多细胞生物的转变发生在大约10亿年前，当时的生物体已经不存在了，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，在生活在池塘里的一种叫做Volvocine藻类的生物中，从单细胞生物到多细胞生物的转变发生在最近，这使得它们现在的近亲中保留了多细胞进化的遗传特征。虽然Volvocine藻类曾经被简单地称为“池塘浮渣”，但它们现在被认为是植物和动物等其他生物的简单形式的代表，因此使它们成为了解多细胞植物和动物如何进化的宝贵工具。现在，Volvocine藻类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，史密森尼博物馆（Smithsonian Museum）也将其作为多细胞进化的主要例子之一。为了确定哪些基因对Volvocine藻类的多细胞性是重要的，将对它们的基因组进行测序和比较，以确定哪些基因在多细胞藻类中与近亲单细胞藻类相比正在进化。一旦确定，这些基因将被独立测试，以确认它们确实是重要的过渡到多细胞。由于Volvocine藻类与包括植物和动物在内的其他生物相似，因此该项目产生的数据对于理解多细胞生物在所有生命领域的进化过程将具有广泛的重要意义。在这个项目的过程中，当地的高中、本科生和其他学员将有机会参与到这项工作中来，包括向一所学生的父母受过大学教育的比例不到20%的高中伸出援手。该项目产生的基因组数据将在Phytozome网站上公开（http://www.phytozome.net），该项目还将为Volvocine藻类的国际教育工作提供额外的数据，Volvocales信息项目（http://www2.unb.ca/vip/）.The多细胞生物的进化是一个主要的进化转变，导致细胞组织和功能的根本变化。然而，多细胞生物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：第一个群体多细胞生物进化时，单个细胞聚集在一起形成一个合作群体；然后，细胞命运的决定演变为两种不同的生殖细胞系和体细胞系，最后，有机体的大小扩大，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潜在的、简洁的遗传变化，这些变化是殖民地合作群体进化、胚体进化和有机体大小进化所必需的。该项目将利用Volvocine藻类作为一个模型系统，它经历了最近的多细胞进化的例子。Volvocales是一个很好的多细胞模式系统，因为成员物种表现出逐步的多细胞特征的增益和损失。该项目的中心假设是，单细胞衣藻中现有的遗传途径在进化过程中随着藻门的复杂性增加而被增选。为了验证这一假设，PI将(a)对代表多细胞化的三个主要步骤的Volvocales基因组内容进行测序和比较，以确定与多细胞化和有机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确定表达模式改变并与Volvocales多细胞化相关的基因。(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候选基因是否积极地引起多细胞性，从而确定候选基因在Volvocales中的功能何时被增选。该项目不仅将确定与从单细胞到多细胞进化相关的基因，而且将挑战该领域的主流假设，该假设认为大规模基因组复制和新功能化事件是多细胞进化的基础。该项目是两个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来自代表性不足群体的高中生和大学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课程的现代化。参加这个项目的高中生将分两个步骤接受培训。首先，pi将向他们的高中合作者提供外联服务，以建立课堂单元，用于教授系统发育分类或生物体的分子基因分型。接下来，学生们将参加周末访问KSU和uof Az，在那里他们将使用他们在课堂上获得的技能进行PCR基因型藻类菌株，这些菌株将用于项目中的种群研究。对科学有浓厚兴趣的学生将有机会在暑期到PI的实验室实习。实习生将前往美国各地，协助分离新的Volvocales菌株进行种群研究，然后利用他们的培训对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分类群，并对水质进行取样测量，为未来的项目做准备。

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.