ATOL: Collaborative Research: Deep Green Plant Phylogenetics: Novel Analytical Methods for Scaling Data from Genomics to Morphology

犹他州州立大学的保罗·沃尔夫博士获得了一笔赠款，用于研究绿色植物的进化。 人类依靠绿色植物来获得食物、住所、衣服和提供生命所必需的氧气。 从生物学的角度来看，作为生命之树中最古老和最多样化的分支之一，绿色植物提供了一个无与伦比的系统，可以探索生物体之间的相互关系，并接近一些关于地球上生命多样化的最重要和最有趣的问题。 这些问题中有许多与基本的进化事件有关，例如生物体从单细胞到多细胞的转变，土地的殖民化以及不同生命周期模式的衍生。因此，了解它们的进化历史是NSF组装生命之树计划的关键组成部分。这笔赠款是一个合作项目的一部分，包括毕格罗海洋科学实验室，加州大学伯克利分校，南伊利诺伊大学，犹他州州立大学，华盛顿大学和耶鲁大学的主要研究人员，重点将是：1）解决绿色植物多样化的主要模式; 2）调查与这些生物的长期进化历史有关的问题; 3）提供一个分析模型，该模型将适用于具有广泛进化历史的其他生物群体。 该小组将强调开发新的分析方法，以便能够在多个尺度上进行分析，并利用来自不同来源的所有现有数据。 一个坚实的骨干关系的基因组和结构的基础上的50-100种植物，代表了关键的深分支谱系，将使更多的植物整合到一个全面的图片绿色植物系谱以前和正在进行的研究。该项目的主要目标是：1）完成叶绿体和线粒体的全基因组序列矩阵，并开发细菌人工染色体（BAC）核基因组文库; 2）为相同的植物产生一套全面的可比较的形态和超微结构数据; 3）使用设计用于允许跨研究缩放的方法，将来自绿色植物系统发育层次的推论纳入其中。通过多种综合培训、教育和外联活动，将不断向科学界和其他方面传播该研究小组的活动和进展，Paul Wolf将协调该项目基因组序列数据的获取。这包括获得适当的植物材料，确保从DNA提取到基因组测序的样本流，填补基因组序列中的空白，将序列数据建立数据库并进入公共领域，以及进行进化分析。

A grant has been awarded to Dr. Paul Wolf of Utah State University to investigate green plant evolution. Humans rely on green plants for food, shelter, clothing, and for providing the oxygen that is essential to life. From a biological perspective and as one of the oldest and most diverse branches of the tree of life, green plants provide an unparalleled system in which to explore interrelationships of living organisms and to approach some of the most significant and intriguing questions concerning the diversification of life on earth. Many of these questions relate to fundamental evolutionary events, such as the transition of organisms from single-celled to multicellular body plans, the colonization of land, and the derivation of different life-cycle modes. Accordingly, understanding their evolutionary history is a critical component in the NSF's Assembling the Tree of Life program.This grant is part of a collaborative project, including principal investigators from the Bigelow Laboratory for Ocean Sciences, the University of California at Berkeley, Southern Illinois University, Utah State University, the University of Washington, and Yale University, the focus will be: 1) resolving the primary pattern of diversification among green plants; 2) investigating questions relating to the long evolutionary history of these organisms; 3) providing a model for analysis that will be applicable to other groups of organisms with extensive evolutionary histories. The team will emphasize the development of novel analytical methods that make it possible to conduct analyses across multiple scales and to use all of the available data from heterogeneous sources. A solid backbone of relationships based on genomes and structure for 50-100 plants, representing the critical deep-branching lineages, will enable the integration of previous and ongoing studies of many more plants into a comprehensive picture of green plant genealogy. The primary objectives of the project are: 1) complete a matrix of whole genome sequences for chloroplasts and mitochondria, and develop Bacterial Artificial Chromosome (BAC) nuclear genome libraries; 2) produce a comprehensive set of comparable morphological and ultrastructural data for the same plants; and 3) incorporate inferences from across the phylogenetic hierarchy in green plants using methods designed to permit scaling across studies. Multiple integrated training, educational and outreach activities will result in continual dissemination of the activities and progress of this research group to the scientific community and beyond.Paul Wolf will coordinate the acquisition of genome sequence data for the project. This includes obtaining appropriate plant material, ensuring sample flow from DNA extraction to genome sequencing, filling in gaps in genome sequences, databasing and entering into public domain the sequence data, and performing evolutionary analyses.