Quantifying the genomic sources of evolutionary innovations through integrative biology

通过综合生物学量化进化创新的基因组来源

• 批准号: RGPIN-2020-04844
• 负责人: Landry, Christian
• 金额: $ 4.74万
• 依托单位: Université Laval
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=744415
• 关键词: Quantifying; genomic; sources; evolutionary; innovations

Background Rapid environmental changes have to be met with molecular innovations. Macroevolution has described how organisms may have colonized new environments over geological time scales. In contrast, we know relatively little about the quantitative features of micro-innovations at the genomic level, i.e. what is their quantitative contribution to phenotypes and fitness, how they first occur in populations and how they are shaped by mutation, natural selection and genetic drift. Moreover, in general, we have access to what happened during evolution but not to what could have happened, i.e. what was available to natural selection and random genetic drift. We will examine these questions at different levels of resolution and at different time scales, using forward evolution and the analysis of evolution back in time. The Study System Because S. cerevisiae has been the core eukaryote model in genomics, cell biology and physiology, the Saccharomyces genus offers a unique opportunity for the manipulation and analysis of genomes in the context of research that wants to navigate from the genome to phenotypes. Their relatively small genomes and rapid evolution allow to explore evolutionary mechanisms to saturation, potentially enabling the full parameterization of the key factors driving evolution. Objectives We will be addressing how novelty comes about in genomes at two time scales. In the first case, we will examine extremely rapid changes that may occur faster than actual base-pair mutation rates, which we think is relevant, for instance in the context of adaptation to extreme conditions that would otherwise lead to extinction. We will examine how species can combine and mix their genomes during inter-species hybridization to propel evolution forward. In the second case, we will focus on a longer time scale, the scale at which populations diverge and become species. In this timescale, we will examine how novel genes evolve in genomes from non-coding sequences. Finally, we will examine how short and long time scale processes can synergize each other. We will gain a better understanding of these processes by analysing natural diversity in the wild and by evolving genomes and populations in the laboratory. We will also harness the latest development in genome editing technologies to examine, one evolutionary change at a time, how molecular novelties such as novel genes evolve and contribute to fitness variation. Novelty and significance: Biology needs a better quantitative understanding of the relationships that link genomes to phenotypes. This research program will draw from the most recent technological developments to provide a major step in this direction. This will provide a strong foundation in terms of how genome organization produces novelty at the genotypic level and how this affects biological systems and their performance.

背景环境的快速变化必须与分子创新相适应。宏观进化描述了生物如何在地质时间尺度上殖民新环境。相比之下，我们对基因组水平上的微创新的数量特征知之甚少，即它们对表型和适合度的数量贡献是什么，它们如何首次出现在种群中，以及它们是如何受到突变、自然选择和遗传漂移的影响的。此外，总的来说，我们可以了解进化过程中发生的事情，但不能了解可能发生的事情，即自然选择和随机遗传漂移的可能性。我们将在不同的分辨率和不同的时间尺度上研究这些问题，使用向前进化和对时间向后进化的分析。由于酿酒酵母一直是基因组学、细胞生物学和生理学中的核心真核细胞模型，因此，在从基因组到表型的研究背景下，酵母属为基因组的操作和分析提供了独特的机会。它们相对较小的基因组和快速进化允许探索达到饱和的进化机制，潜在地使推动进化的关键因素能够完全参数化。目的我们将在两个时间尺度上讨论基因组中的新颖性是如何产生的。在第一种情况下，我们将研究可能比实际碱基对突变率更快发生的极快变化，我们认为这是相关的，例如在适应否则将导致灭绝的极端条件的背景下。我们将研究物种如何在物种间杂交期间结合和混合它们的基因组，以推动进化。在第二种情况下，我们将关注更长的时间尺度，即种群分化并成为物种的尺度。在这个时间表中，我们将研究新基因是如何从非编码序列在基因组中进化的。最后，我们将研究短时间尺度过程和长时间尺度过程如何相互协同。我们将通过分析野生环境中的自然多样性以及在实验室中进化基因组和种群来更好地了解这些过程。我们还将利用基因组编辑技术的最新发展，一次检查一个进化变化，研究新基因等分子新颖性是如何进化的，并有助于适应能力的变化。新颖性和意义：生物学需要更好地量化了解将基因组与表型联系起来的关系。这项研究计划将借鉴最新的技术发展，在这一方向上迈出重要的一步。这将为基因组组织如何在基因水平上产生新颖性以及如何影响生物系统及其性能提供坚实的基础。