The origin of plants: genomes, rocks, and biochemical cycles

植物的起源：基因组、岩石和生化循环

• 批准号: NE/N003438/1
• 负责人: Philip Donoghue
• 金额: $ 34.07万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FN003438%2F1
• 关键词: origin; plants; genomes; rocks; biochemical

There can be no doubt that early land plant evolution transformed the planet but how our knowledge of how this happened is in disarray. The clear coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 is an artefact of the absence of earlier terrestrial rocks, and disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles requires a new understanding of early land plant evolution and the timescale over which it was effected. Early life on land was mostly microbial, but sometime between about 700 million and 420 million years ago plants moved from water onto land. The timeframe is controversial and as currently understood it is very broad, but a more precise knowledge of the events is key to linking the early evolution of plant life to major environmental change. Ambiguity and uncertainty arise because the principal lines of evidence conflict. Fossils, notably plant microfossils (spores), point to colonization beginning about 470 Ma (million years ago), but the affinities of the early spore producers are controversial. Macrofossils (plant stems, multicellular organ systems, etc) indicate a later colonization, beginning about 430 Ma. Calibrated molecular phylogenies - studies of the timing of divergence of living plant lineages based on molecular sequence data, where the rate of mutation is calibrated to time using fossils - point to an origin and early evolution of life on land that may have begun during the Late Neoproterozoic, long predating the fossil evidence. Recent research has identified difficulties with both molecular phylogenetic and palaeontological approaches, which our proposed research program will address. We have assembled a multidisciplinary team to conduct research to remedy these shortcomings. We will establish a robust genealogy for living plant lineages based on a genome-scale amount of molecular sequence data (~1,000s genes and, therefore, ~1,000,000s nucleotides). The genealogy will be linked to time by including important and exceptionally preserved fossil species. These will be correctly placed through detailed characterization of their anatomy using state of the art Synchrotron Computed Tomography, a novel approach that we have recently shown to provide valuable new data in a recent proof of concept study. Sedimentary regime is known to affect the age estimate given by fossils, so we will also apply new methods develop by us to assess and to correct for this. Together, these approaches will enable us to develop a robust phylogeny calibrated with greater precision to time, which we will use to investigate the evolutionary assembly of key land plant organs and tissue systems (e.g., roots, stomata, vascular tissue, leaves) and their impact on major biogeochemical cycles. Finally, we will we will explore the implications of our plant evolutionary timescale within a leading computer model of global biogeochemical cycling (GENIE). This will enable us to generate predictions for levels of atmospheric carbon dioxide levels and of organic carbon productivity that we will test against geological observations. Ultimately, we will establish a new scenario for the timing and tempo of early land plant evolution, the assembly of land plant bodyplans, and a new understanding of the effect of this episode upon the evolution of the Earth System.

毫无疑问，早期的陆地植物进化改变了地球，但我们对这是如何发生的知识是混乱的。陆地植物化石的首次出现和大气中氧气和CO2的形成变化的明显巧合是早期陆地岩石不存在的假象，解开陆地植物体平面组装的时间及其对全球地球化学循环的影响需要对早期陆地植物进化及其影响的时间尺度有新的认识。早期的陆地生命主要是微生物，但在大约7亿到4.2亿年前的某个时候，植物从水中迁移到陆地上。时间框架是有争议的，目前理解它是非常广泛的，但更精确的知识的事件是关键联系植物生命的早期进化的主要环境变化。由于证据的主线相互冲突，出现了模棱两可和不确定性。化石，特别是植物微体化石（孢子），指出殖民开始约470 Ma（百万年前），但早期孢子生产者的亲和力是有争议的。大型化石（植物茎，多细胞器官系统等）表明殖民后期，开始约430 Ma。校准的分子遗传学-基于分子序列数据对活植物谱系分化时间的研究，其中突变率使用化石校准时间-指出陆地生命的起源和早期进化可能始于晚新元古代，早于化石证据。最近的研究发现，分子系统发育和古生物学的方法，我们提出的研究计划将解决的困难。我们已经组建了一个多学科团队来进行研究，以弥补这些缺陷。我们将基于基因组规模的分子序列数据（约1，000个基因，因此约1，000，000个核苷酸）为活植物谱系建立一个强大的系谱。家谱将通过包括重要和特别保存的化石物种与时间联系起来。这些将通过使用最先进的同步加速器计算机断层扫描技术对其解剖结构进行详细表征来正确放置，这是一种新的方法，我们最近在最近的概念验证研究中证明了这种方法可以提供有价值的新数据。众所周知，沉积状态会影响化石给出的年龄估计，因此我们也将应用我们开发的新方法来评估和纠正这一点。总之，这些方法将使我们能够开发出一种鲁棒的、对时间具有更高精度的校准的植物发生学，我们将用它来研究关键陆地植物器官和组织系统的进化组装（例如，根、气孔、维管组织、叶）及其对主要生物地球化学循环的影响。最后，我们将探索我们的植物进化时间尺度内的全球地球化学循环（GENIE）领先的计算机模型的影响。这将使我们能够预测大气二氧化碳水平和有机碳生产力的水平，我们将根据地质观测进行测试。最终，我们将建立一个新的场景，早期陆地植物进化的时间和克里思，陆地植物的总体规划，以及对这一事件对地球系统进化的影响的新理解。

项目成果

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution.

• DOI: 10.1111/nph.15011
• 发表时间: 2018-04
• 期刊: The New phytologist
• 作者: Barba-Montoya J;Dos Reis M;Schneider H;Donoghue PCJ;Yang Z
• 通讯作者: Yang Z

Cryogenian Origins of Multicellularity in Archaeplastida

• DOI: 10.1093/gbe/evae026
• 发表时间: 2024-02-22
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Bowles，Alexander M. C.;Williamson，Christopher J.;Donoghue，Philip C. J.
• 通讯作者: Donoghue，Philip C. J.

Genome of the glacier alga Ancylonema and its insights into the evolution of streptophyte life on ice and land

• DOI: 10.1101/2023.10.20.563300
• 发表时间: 2023-10
• 期刊: bioRxiv
• 作者: Alexander M. C. Bowles;T. Williams;P. Donoghue;Douglas A. Campbell;Christopher J. Williamson

Constraining Whole-Genome Duplication Events in Geological Time.

限制地质时期的全基因组复制事件。

• DOI: 10.1007/978-1-0716-2561-3_7
• 发表时间: 2023
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Clark JW

Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.

基因组和化石的综合证据揭示了生命的早期进化和真核生物的起源。

• DOI: 10.1038/s41559-018-0644-x
• 发表时间: 2018-10
• 期刊: Nature ecology & evolution
• 影响因子: 16.8
• 作者: Betts HC;Puttick MN;Clark JW;Williams TA;Donoghue PCJ;Pisani D
• 通讯作者: Pisani D