OPUS: Genome doubling in an evolutionary model: Synthesis across biological and temporal scales

基因组加倍，即细胞中所有遗传信息的加倍，是产生地球上大部分物种多样性的主要进化力量。甚至人类基因组也有重复的片段，这是数亿年前早期脊椎动物的古老基因组加倍的结果。虽然它发生在动物和真菌中，但基因组加倍在植物中特别常见。经历了基因组加倍的生物体通常比它们的非复制亲本更成功，并具有新的性状;例如，具有加倍基因组的植物通常比它们的亲本更大，并产生更多的果实和种子。事实上，大多数农作物和世界上最糟糕的杂草都起源于这个过程。因此，基因组加倍在生态学和经济学上都非常重要，但科学家们还不知道重复基因的存在如何产生新的性状。尽管这一过程的最早阶段对于了解基因和性状之间的联系最为关键，但正是这些早期阶段最难研究，主要是因为几乎所有基因组加倍事件都发生在非常遥远的过去，即数百万年前。在这个项目中，研究人员将通过关注向日葵家族中的两种植物来研究这些早期阶段，这两种植物在过去90年中通过基因组加倍在自然界中形成。这些物种的独特之处在于它们的起源时间是如此之近;因此，它们是了解基因组加倍如何产生新性状以及如何利用这一过程来解决与粮食安全，人类健康和气候变化有关的社会问题的完美模型。全基因组复制（WGD，或多倍体）是一个主要的进化力量，但多倍体进化的关键早期阶段仍然知之甚少。该项目将通过分析过去30年来为Tragopogon编制的数据，对重复多倍体形成和基因组合并的后果提供新的见解，从而促进对WGD的新理解，Tragopogon是向日葵家族的一种植物，包括两个最近（约90岁）和重复形成的天然异源四倍体（T。mirus，T. miscellus）及其二倍体亲本（T. Albertus，T. pratensis、T. porrifolius）。将应用新工具，包括通过CRISPR-Cas9进行遗传操作，并将获得基因组和转录组的新长读段序列数据，以最大限度地发挥现有数据的价值。解决WGD基本问题的新分析将集中在：1）多倍体及其二倍体亲本的自然群体分布; 2）从欧洲到美国的二倍体亲本介绍; 3)不同来源的四倍体之间的可交配性; 4）多倍体形成的遗传/基因组后果（转录组;参考基因组;蛋白质组;选择性剪接）; 5）合成系的特性;以及6）多倍体及其二倍体亲本的生态学比较（温室数据;生态位建模）。重点将放在综合关于在婆罗门参和其他系统中的WGD早期阶段的信息，包括天然和合成的。这一广泛的综合研究不仅将为WGD提供新的见解，而且还为不同研究人员的未来研究奠定了基础，以调查WGD后基因组进化的模式、克里思、机制和驱动力。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

Genome doubling, which doubles all genetic information in a cell, is a major evolutionary force that has produced much of the species diversity on Earth. Even the human genome has duplicated segments that result from ancient genome doubling in early vertebrates hundreds of millions of years ago. Although it occurs in animals and fungi, genome doubling is particularly common in plants. Organisms that have undergone genome doubling are often more successful than their non-duplicated parents and have new traits; for example, plants with doubled genomes are often larger than their parents and produce more fruits and seeds. In fact, most agricultural crops and the world’s worst weeds have all originated through this process. As a result, genome doubling is very important both ecologically and economically, yet scientists do not yet understand how the presence of duplicated genes produces new traits. Although the earliest stages of this process are the most critical for understanding the connection between genes and traits, it is precisely these early stages that are the most difficult to study, mainly because nearly all genome doubling events occurred in the very distant past, millions of years ago. In this project, the researchers will investigate these early stages by focusing on two species of plants in the sunflower family that formed in nature via genome doubling in the past 90 years. These species are unique in that their time of origin is so recent; as a result, they are perfect models for learning about how genome doubling generates new traits and how this process can be used to address societal problems related to food security, human health, and climate change. Whole-genome duplication (WGD, or polyploidy) is a major evolutionary force, yet the critical early stages of polyploid evolution remain poorly understood. This project will promote novel understanding of WGD by providing new insights into recurring polyploid formation and the consequences of genomic merger through analysis of data compiled over the past 30 years for Tragopogon, a genus of plants from the sunflower family that includes two recently (~90 years old) and repeatedly formed natural allotetraploids (T. mirus, T. miscellus) and their diploid parents (T. dubius, T. pratensis, T. porrifolius). New tools, including genetic manipulation via CRISPR-Cas9, will be applied, and new long-read sequence data for both genomes and transcriptomes will be acquired to maximize the value of available data. New analyses to address fundamental questions regarding WGD will focus on: 1) Distribution of natural populations of the polyploids and their diploid parents; 2) Introductions of the diploid parents from Europe to U.S.; 3) Crossability between tetraploids of separate origin; 4) Genetic/genomic consequences of polyploid formation (transcriptomes; reference genomes; proteomes; alternative splicing); 5) Properties of synthetic lines; and 6) Ecological comparisons of polyploids and their diploid parents (greenhouse data; niche modeling). Emphasis will be placed on synthesizing information on the early stages of WGD in Tragopogon and other systems, both natural and synthetic. This broad synthesis will not only provide new insights into WGD, but also set the stage for future investigations by diverse researchers to investigate the patterns, tempo, mechanisms, and forces driving and shaping post-WGD genome evolution.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.